Engineered shell proteins for microcompartment shell electron transfer and catalysis

ABSTRACT

Described herein are bacterial microcompartments shell proteins modified to stably incorporate iron-sulfur clusters. Such bacterial microcompartments shell proteins exhibit redox cycling and confer electron transfer functionality to bacterial microcompartment shells.

RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No. 15/851,382, now U.S. Pat. No. 10,479,999, filed Dec. 21, 2017, which claims benefit of priority to the filing date of U.S. Provisional Application Ser. No. 62/438,655, filed Dec. 23, 2016, the contents of which are specifically incorporated herein by reference in their entity.

FEDERAL FUNDING

This invention was made with government support under DE-FG02-91ER20021 awarded by the U.S. Department of Energy. The government has certain rights in the invention.

BACKGROUND OF THE INVENTION

Microbes have been used for many manufacturing purposes, including for energy production and the production of useful materials. With growing greenhouse-gas emissions, scientists are seeking better pathways to produce biofuels and other chemicals such as bioplastics. Although bacteria can be engineered to make all sorts of compounds and materials, the efficiencies of such methods are not optimal and the isolation of those compounds and materials can be laborious.

SUMMARY

Bacterial microcompartments (BMCs) are organelles used by various bacteria to encapsulate metabolic pathways into a proteinaceous shell. As illustrated herein, bacterial microcompartments can provide self-assembling modules, scaffold reactions in three dimensions, optimize reactions and stabilize enzymes in their lumens, and serve as catalytic bioreactors that can be customized to support new metabolic functions.

DESCRIPTION OF THE FIGURES

The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.

FIG. 1 schematically illustrates the organization of a bacterial microcompartment (BMC) shell and the composition of a BMC shell. For clarity, only one facet of the icosahedron is tiled with shell proteins BMC-H (blue hexagon), BMC-T (red hexagon with larger hole in the middle), and BMC-P (yellow pentagon).

FIGS. 2A-2G illustrate structural features of a BMC-T1 component of a BMC shell and biochemical characterization of BMC-T1-S55C. FIG. 2A illustrates the structure of BMC-T1 in three orientations. The convex face of the trimer is shown on the left, the concave side on the right. Each protomer is represented in a different color. FIG. 2B illustrates O_(γ)-O_(γ) trigonal distances between the side chains of the Ser55 residues converging at the three-fold symmetry axis (pore). FIG. 2C illustrates a side view of the pore region, showing the orientation of the side chains of the Ser55 residues (orange sticks identified by black arrows) towards the concave face. FIG. 2D shows refined 2F_(o)-F_(c) electron density maps of residues surrounding the three-fold symmetry axis in the BMC-T1 trimer. Electron density map contoured at 1 σ. Left: concave and right: convex surface of the BMC-T1 trimer. Ser55 residues are shown in orange. The density in the pore could not be assigned and is presumably a buffer or a salt molecule. FIG. 2E shows the colors of purified BMC-T1 (left) and purified BMC-T1-S55C (right). FIG. 2F shows a SDS gel stained using Coomassie Blue showing the purity of BMC-T1-S55C (arrow). FIG. 2G illustrates a typical size exclusion chromatogram obtained for BMC-T1-S55C. Similar chromatograms were obtained for BMC-T1. The arrow corresponds to a molecular weight of 69 kDa (calculated molecular weight of a monomer, 21.9 kDa). The first and last peaks are contaminants and do not contain any BMC-T1-S55C protein. Inset: calibration curve using standards of molecular weight 66 kDa (bovine serum albumin), 44 kDa (ovalbumin) and 17 kDa (myoglobin).

FIGS. 3A-3G illustrate the structure of BMC-T1-S55C. FIG. 3A shows a side view of the structure showing the [4Fe-4S] cluster (yellow and orange sticks). FIG. 3B shows an expanded view of the three-fold symmetry axis (pore region) showing the [4Fe-4S]cluster with the water molecule (red sphere) as the fourth unique iron ligand (black dashed line). Red dashed lines represent hydrogen bonds between the backbone amide of Gly155 and the sulfur atom of Cys55 while yellow dashed lines represent hydrogen bonds between the backbone amide of Ala157 and the cluster sulfides. FIG. 3C illustrates electrostatic rendering of the BMC-T1-S55C trimer. Electrostatic surfaces are colored between −5 kT/e (red) and +5 kT/e (blue). FIG. 3D shows a 2Fo-Fc map (blue mesh) of the pore region of BMC-T1-S55C contoured at 1 σ. Iron ions are orange, and sulfides are yellow. FIG. 3E shows a simulated annealing omit (Fo-Fc) map of the [4Fe-4S] cluster at the BMC-T1-S55C trimer pore contoured at 3 rmsd/0.32 e⁻/A³ with a rigid body fitted model of the [4Fe-4S] cluster (iron ions grey, sulfides green). FIG. 3F shows an anomalous difference electron density (red mesh) at the site of the iron atoms in the [4Fe-4S] cluster in BMC-T1-S55C, contoured at 4 σ (iron ions, orange, and sulfides, yellow). FIG. 3G illustrates structural superposition of BMC-T1 (dark grey) and BMC-T1-S55C (gold). The Ser55/Cys55 residues are circled, and the [4Fe-4S] cluster is represented as yellow and orange sticks.

FIGS. 4A-4E show UV-Visible and EPR spectra of BMC-T1 and BMC-T1-S55C. FIG. 4A shows UV-Vis spectra where the solid line is the spectrum of BMC-T1-S55C as-isolated after reconstitution; the dashed line is the spectrum of BMC-T1-S55C after reconstitution and incubation with 0.5 mM dithionite; the dotted line is the spectrum of BMC-T1. The spectra were recorded at pH 7.5 and under anaerobic conditions for BMC-T1-S55C. FIG. 4B shows X-Band CW EPR spectra of BMC-T1 (top) and chemically reconstituted BMC-T1-S55C (bottom) after reduction with dithionite. The spectrum of BMC-T1 was recorded at 14 K. The spectra of BMC-T1-S55C were recorded at three different temperatures: 14 K (red trace), 27 K (black trace) and 47 K (blue trace) to demonstrate the relaxation behavior of the [4Fe-4S]¹⁺ signal. Experimental conditions: microwave frequency of 9.481 GHz, microwave power of 0.64 mW, modulation amplitude of 0.6 mT. FIG. 4C shows UV-Vis spectra of BMC-T1-S55C before and after reconstitution of the [4Fe-4S] cluster. The spectra were normalized at an optical density (280 nm) of 1 for comparison. FIG. 4D illustrates characterization of the [4Fe-4S] cluster in BMC-T1-S55C by continuous wave (CW) X-Band EPR spectra of three different preparations of BMC-T1-S55C, both in non-reconstituted (red trace) and reconstituted (blue trace) forms, after reduction with dithionite. Experimental conditions: microwave frequency of 9.481 GHz, microwave power of 0.64 mW, modulation amplitude of 0.6 mT, and temperature of 10 K. The vertical dashed line highlights the position of the g_(z) component of the [4Fe-4S]¹⁺ cluster. FIG. 4E shows CW X-Band EPR spectra of non-reconstituted and reconstituted BMC-T1-S55 prior to and after addition of dithionite. The top EPR spectra (4E-1) show spectra of non-reconstituted BMC-T1-S55C in the absence (blue trace) and the presence of 10 mM dithionite (grey trace). The asterisk denotes a background signal from the resonator cavity. The bottom EPR spectra (4E-2) show spectra of reconstituted BMC-T1-S55C recorded on samples prior (red trace) and after (black trace) reduction with 10 mM dithionite. Experimental conditions: microwave frequency of 9.480 GHz, microwave power of 0.64 mW, modulation amplitude of 0.6 mT, and temperature of 14 K.

FIGS. 5A-5B illustrate reduction potential of the BMC-T1-S55C [4Fe-4S] cluster by spectroelectrochemistry and redox reversibility. FIG. 5A illustrates the percentage of reduced protein as plotted versus the potential, and fitted using a single electron Nernst equation. The calculated E_(m) is −370 mV vs. SHE at pH 7.5 and 25° C. FIG. 5B illustrates re-oxidation of the [4Fe-4S] cluster of BMC-T1-S55C after the redox titration. Spectra were recorded before the titration (using dithionite to reduce the cluster, solid blue line), after full reduction (dashed black line), and after re-oxidation using duroquinone (dotted black line). The additional observed signals in the dithionite-reduced spectrum are the contribution of the reduced redox mediator dyes. The solid blue and dotted black traces are essentially superimposable.

FIGS. 6A-6F illustrate chemical denaturation of BMC-T1 and BMC-T1-S55C. FIG. 6A illustrates CD spectra of BMC-T1 (circle symbols) and [4Fe-4S] cluster-bound BMC-T1-S55C (square symbols) before denaturation displaying two negative bands at 222 and 208 nm and a positive band at 195 nm, demonstrating α-helical and β-sheet structure, respectively. FIG. 6B illustrates chemical denaturation plot of BMC-T1 (circle symbols) and BMC-T1-S55C (square symbols). Denaturation was tracked at 222 nm. FIG. 6C illustrates CD spectra of BMC-T1-S55C at different urea concentrations, which all contained the same protein concentration of 8 μM. These spectra were collected during the denaturation study. FIG. 6D illustrates a UV-Vis spectrum of BMC-T1-S55C after the titration (10.2 M urea final concentration) showing the presence of the [4Fe-4S] cluster at 385 nm. The spectrum was normalized to an optical density at 280 nm of 1. FIG. 6E-6F illustrate responses of BMC-T1-S55C exposed to atmospheric oxygen. FIG. 6E illustrates generation of a [3Fe-4S]¹⁺ cluster upon exposure of BMC-T1-S55C to air for variable times as monitored by EPR spectroscopy. The spectra correspond to a sample of the S55C-modified BMC variant as purified (without dithionite) under O₂-free conditions (red trace), after exposure to air at room temperature for 5 min (blue trace), 30 min (black trace) and 60 min (magenta trace). Experimental conditions: microwave power of 0.64 mW, modulation amplitude of 0.63 mT, temperature of 10° K, microwave frequency=9.480 GHz. FIG. 6F shows UV-Vis spectra of the cluster exposed to air for variable times. Bands at 310-330 nm and 465 nm are typical of [2Fe-2S] clusters.

FIGS. 7A-7C show views of the pore region structure at the three-fold symmetry axis of a BMC-T1 trimer. FIG. 7A shows a face view of the pore region. FIG. 7B shows a side view of the pore region. The Ser55 residues (orange sticks) are oriented towards the concave face. The Ser56 residues (yellow sticks) are oriented towards the convex face. The Ile154 residues (red sticks) are located in the concave face, in the vicinity of the Ser55 residues. FIG. 7C shows a rear view (pore region) of a model of BMC-T1-S55C/I154F based on the structure of BMC-T1-S55C. The [4Fe-4S] cluster is represented as yellow and orange sticks, while modeled F154 residues are represented as grey sticks.

FIGS. 8A-8E illustrate structural and functional features of several variants of BMC-T1 binding [4Fe-4S] clusters. FIG. 8A shows the colors of purified BMC-T1 variants, from left to right: BMC-T1-S55C, BMC-T1-S56C, BMC-T1-S55C/S56C. Protein concentration varies between the different samples. FIG. 8B shows an expanded view of the three-fold symmetry axis of the pore region structure of the BMC-T-S55C/S56. Red dashed lines represent hydrogen bonds between the backbone amide of Gly155 and the sulfur atom of Cys55 while yellow dashed lines represent hydrogen bonds between the backbone amide of Ala157 and the cluster sulfides. Black dashed lines represent the S_(γ)-S_(γ) trigonal distances (5.5 to 5.7 Å) between the side chains of the Cys56 residues converging at the three-fold symmetry axis (pore). This represents a binding site for the cluster present in BMC-T1-S56C. FIG. 8C shows X-Band CW EPR spectra of BMC-T1 (top) and chemically reconstituted BMC-T1-S55C. BMC-T1-S56C and BMC-T1-S55C/S56C after reduction with dithionite. The spectra were recorded at 14 K. Experimental conditions: microwave frequency of 9.481 GHz, microwave power of 0.64 mW, modulation amplitude of 0.6 mT. FIG. 8D shows a UV-Vis spectrum of BMC-T1-S56C after reconstitution of the [4Fe-4S] cluster, before (blue line) and after (red line) reduction using dithionite. FIG. 8E shows a UV-Vis spectrum of BMC-T1-S55C/S56C after reconstitution of the [4Fe-4S] cluster, before (blue line) and after (red line) reduction using dithionite. The spectra shown in FIGS. 8D-8E were recorded at pH 7.5 under anaerobic conditions, and normalized at an optical density (280 nm) of 1 for comparison.

FIG. 9 shows a SDS-PAGE of purified Wild-Type (WT) shells, and purified shells containing engineered BMC-T1 proteins (BMC-T1-S55C, BMC-T1-S56C and BMC-T1-S55C/S56C). Molecular weight (MW) size markers are indicated in kDa on the left.

FIGS. 10A-10G show features of several BMC-T1 variants binding [4Fe-4S] clusters that include the I154F mutation. FIG. 10A shows the colors of purified BMC-T1 variants, shown from left to right: BMC-T1-S55C/I154F. BMC-T1-S56C/I154F, BMC-T1-S55C/S56C/I154F. Protein concentration varies between the different samples. FIG. 10B shows a UV-Vis spectrum of BMC-T1-S55C/I154F after reconstitution of the [4Fe-4S] cluster, before (blue line) and after (red line) reduction using dithionite. FIG. 10C shows a UV-Vis spectrum of BMC-T1-S56C/I154F after reconstitution of the [4Fe-4S] cluster, before (blue line) and after (red line) reduction using dithionite. FIG. 10D shows a UV-Vis spectrum of BMC-T1-S55C/S56C/I154F after reconstitution of the [4Fe-4S] cluster, before (blue line) and after (red line) reduction using dithionite. The spectra shown in FIGS. 10B-10D were recorded at pH 7.5 under anaerobic conditions, and normalized at an optical density (280 nm) of 1 for comparison. FIG. 10E shows X-Band CW EPR spectra of BMC-T1-S55C/I154F after reduction with dithionite, as purified (red trace) and after chemical reconstitution of the [4Fe-4S] cluster (blue trace). FIG. 10F shows X-Band CW EPR spectra of BMC-T1-S56C/154F after reduction with dithionite, as purified (red trace) and after chemical reconstitution of the [4Fe-4S] cluster (blue trace). FIG. 10G shows X-Band CW EPR spectra of BMC-T1-S55C/S56C after reduction with dithionite, as purified (red trace) and after chemical reconstitution of the [4Fe-4S] cluster (blue trace). Other experimental conditions for the spectra shown in FIG. 10E-10G: modulation amplitude: 0.6 mT, points 2048, scan time 169 s, temperature 10 K, microwave power 1 mW.

FIG. 11A-11B graphically illustrate the reduction potential of BMC-T1 [4Fe-4S] variants where the percentage of reduced protein is shown versus the solution potential, as detected by spectroelectrochemistry and fit using the Nernst equation. FIG. 11A graphically illustrates the reduction potential of the BMC-T1-S55C, BMC-T1-S56C and BMC-T1-S55C/S56C [4Fe-4S] clusters. FIG. 11B graphically illustrates the reduction potential of the BMC-T1-S55C/I154F [4Fe-4S] cluster. The calculated E_(m) were −370 mV, −455 mV, −310 mV and −460 mV vs. SHE at pH 7.5 and 25° C., for BMC-T1-S55C, BMC-T1-S56C. BMC-T1-S55C/S56C and BMC-T1-S55C/I154F respectively.

DETAILED DESCRIPTION

Described herein are bacterial microcompartment shell proteins that have been modified to include cysteine residues for incorporation of metals (e.g. iron-sulfur clusters) into the bacterial microcompartment shells. Such modified bacterial microcompartments can, for example, have a reduction potential of −500 to −200 mV, or −455 to −370 mV versus the Standard Hydrogen Electrode (SHE). For example, as illustrated herein, the reduction potential of the engineered [4Fe-4S] cluster in BMC-T1-S55C (SEQ ID NO:3) is −370 mV versus the Standard Hydrogen Electrode (SHE). Other mutants were designed to fine-tune this reduction potential value: −455 mV and −310 mV versus SHE for BMC-T1-S56C (SEQ ID NO:4) and BMC-T1-S55C/S56C (SEQ ID NO:5) respectively. These clusters have also been shown to be redox active and stable through redox cycling. Furthermore, the substitution of an isoleucine residue in the vicinity of the [4Fe-4S] cluster with a phenylalanine residue creates a hydrophobic environment around the cluster that is useful for the fine-tuning of the reduction potential of the cluster. Hence, the modifications to bacterial microcompartment shell proteins confer electron transfer functionality to bacterial microcompartment shells. Such modifications can be fine-tuned to confer new catalytic activities to microcompartment shell proteins.

Modified bacterial microcompartments described herein therefore introduce electron transfer functionality into bacterial microcompartment shells. This can support encapsulation of oxidoreductive pathways. A bacterial microcompartment shell protein BMC-T1 from H. ochraceum was engineered to have point mutation that allow the microcompartments to bind metals such as iron-sulfur clusters. These metal containing microcompartment shell proteins, when incorporated, can transfer electrons (oxidation-reduction cycles) from one side of the bacterial microcompartment to the other. The constructs described herein provide different varieties of the modified BMC-T1 protein through specific point mutations in the interprotein pore, which enables several redox potentials to cater to various needs.

Bacterial microcompartments can also serve as nanobiocatalytic reactors in vivo or in vitro. For example, the modified bacterial microcompartments can also encapsulate a nitrogenase so that the combination of nitrogenase and the redox reactions can improve nitrogen fixation. The modified bacterial microcompartments can also encapsulate one or more enzymes of the methylerythritol 4-phosphate (MEP) pathway (e.g., IspG and IspH) to improve production of the basic building blocks for the biosynthesis of terpenes. Such terpenes include numerous chemicals (more than 55.000 are known) that provide starting materials and intermediates for production of pharmaceuticals, biofuels, fragrances and more. For example, IspG and IspH are [4Fe-4S] cluster enzymes that could use electrons transferred by engineered shell proteins for their catalytic activity. IspG and IspH are generally sensitive to oxygen and not very catalytically efficient; encapsulation in a microcompartment shell protects them from oxygen and can improve their efficiency. In another example, the modified bacterial microcompartments can also include NAD/NADP, which can transform the modified microcompartments and/or host cells that have such modified microcompartments into bio-batteries.

Modification of Bacterial Microcompartments

The modified bacterial microcompartment shell proteins described herein have one or more cysteine residues incorporated into them. For example, one or more amino acids that line the shell protein pore can be replaced with one or more cysteine residues. In some cases, two or more amino acids within the microcompartment pore can be replaced with two or more cysteine residues. In some cases, three or more amino acids within the microcompartment pore can be replaced with three or more cysteine residues. The position of the substituted residues, which coordinate with or are in the vicinity of the redox active metal, can be varied to alter metal selectivity and/or midpoint potential.

Any amino acid within a microcompartment shell protein can be replaced to provide the modified microcompartment proteins. For example, any of the following amino acids within microcompartment shell proteins can be replaced: serine, threonine, valine, leucine, isoleucine, methionine, aspartic acid, asparagine, alanine, arginine, aspartic acid, glutamic acid, glutamine, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, tryptophan or tyrosine. In some cases, the amino acid is not aspartic acid, isoleucine, leucine, or methionine. In some cases, when an amino acid is replaced by a cysteine, the replace amino acid can be about the same size as a cysteine residue. Cysteine has a molecular weight of 103.15 g/mole and the following structure.

Examples of amino acids that can be replaced by cysteine in the modified bacterial microcompartments include serine, threonine, valine, leucine, isoleucine, methionine, aspartic acid, and asparagine as well as other amino acid substitutions.

The site(s) of amino acid replacement within the bacterial microcompartment shells include sites that project amino acid side chains of the replacement amino acids into the interior or to the exterior of the microcompartments. In some cases, the site(s) of amino acid replacement within the bacterial microcompartments include sites that are within the microcompartments or are near one or more pore openings of the microcompartments.

A bacterial microcompartment shell typically has three different types of proteins that serve as its basic building blocks (see FIG. 1). BMC-H subunits (single Pfam00936 domain) assemble into a cyclic hexamer. Tandem (BMC-T) proteins consist of a fusion of two Pfam00936 domains. BMC-T trimers form a pseudohexamer (Klein et al., J. Mol. Biol. 392: 319 (2009); Sagermann et al., Proc. Natl. Acad. Sci. U.S.A. 106: 8883 (2009).

BMC-P proteins (single Pfam03319 domain) assemble into pentamers that cap the vertices of an apparently icoshedral shell (FIG. 1: Tanaka et al. Science 319: 1083 (2008); Sutter et al., Photosynth. Res. 118: 9 (2013)); and Wheatley et al., Protein Sci. 22: 660 (2013)). The shell protein oligomers typically contain pores at the symmetry axis that are proposed to function as selective conduits for the diffusion of metabolites (substrates and products) into and out of the BMC lumen (Kerfeld et al., Science 309: 936 (2005); and Kinney et al., Photosynth. Res. 109: 21 (2011)).

An example of a Haliangium ochraceum BMC-T1 (Hoch_5812) has the following amino acid sequence (SEQ ID NO: 1).

  1 MDHAPERFDA TPPAGEPDRP  ALGVLELTSI ARGITVADAA  41 LKRAPSLLLM

LMMRGQVAEV EESMIAAREI  81 AGAGSGALLD ELELPYAHEQ LWRFLDAPVV ADAWEEDTES 121 VIIVETATVC AAIDSADAAL  KTAPVVLRDM RLAIGIAGKA 161 FFTLTGELAD VEAAAEVVRE  RCGARLLELA CIARPVDELR 181 GRLFF A nucleotide segment encoding the SEQ ID NO: 1 BMC-T1 protein with SEQ ID NO: 1 can, for example, have the nucleotide sequence shown below as SEQ ID NO:2.

1 ATGGACCACG CTCCGGAACG CTTTGATGCG ACCCCGCCGG 41 CAGGTGAACC GGACCGCCCG GCACTGGGTG TGCTGGAACT 81 GACCTCAATT GCTCGTGGTA TCACCGTTGC GGATGCGGCC 121 CTGAAACGTG CACCGAGTCT GCTGCTGATG TCCCGCCCGG 161 TCAGCTCTGG CAAGCATCTG CTGATGATGC GTGGCCAGGT 201 GGCAGAAGTT GAAGAATCAA TGATTGCAGC TCGCGAAATC 241 GCTGGTGCAG GTTCGGGTGC TCTGCTGGAT GAACTGGAAC 281 TGCCGTATGC GCACGAACAA CTGTGGCGCT TTCTGGACGC 321 ACCGGTGGTT GCAGATGCAT GGGAAGAAGA CACCGAAAGC 361 GTCATTATCG TGGAAACCGC GACGGTGTGC GCGGCCATTG 401 ATAGTGCCGA CGCAGCTCTG AAAACGGCAC CGGTCGTGCT 441 GCGTGATATG CGCCTGGCCA TTGGTATCGC TGGCAAGGCG 481 TTTTTCACCC TGACGGGTGA ACTGGCAGAC GTGGAAGCGG 521 CCGCAGAAGT TGTCCGTGAA CGTTGCGGTG CACGTCTGCT 561 GGAACTGGCA TGTATCGCAC GCCCGGTTGA TGAACTGCGT 601 GGCCGCCTGT TTTTCTAA

A modification of such a BMC-T1 structure involving substitution of serine at position 55 with a cysteine (S55C) was made in the BMC-T1 gene using the QuikChange Lightning site-directed mutagenesis kit (Agilent Technologies). An amino acid sequence for such a S55C-modified BMC-T1 (BMC-T1-S55C) protein is as follows (SEQ ID NO:3).

  1 MDHAPERFDA TPPAGEPDRP  ALGVLELTSI ARGITVADAA  41 LKRAPSLLLM

LMMRGQVAEV EESMIAAREI  81 AGAGSGALLD ELELPYAHEQ LWRFLDAPVV ADAWEEDTES 121 VIIVETATVC AAIDSADAAL  KTAPVVLRDM RLAIGIAGKA 161 FFTLTGELAD VEAAAEVVRE  RCGARLLELA CIARPVDELR 181 GRLFF

As illustrated herein, the BMC-T1-S55C monomer scaffold is composed of two domains which have complementary roles for interaction with metal atoms. The first domain harbors the [4Fe-4S] cluster-binding site (Cys55), while residues within the second domain (Gly155 and Ala157) provide hydrogen bonding interactions that most likely stabilizes the [4Fe-4S] cluster and facilitates its redox reversibility. In most [Fe—S] cluster proteins, the cluster ligands are on the same polypeptide chain; in contrast, each BMC-T1-S55C protomer contributes one-third of the [4Fe-4S] cluster binding site, which is completed by the trimerization. As observed in other systems, three cysteine ligands are sufficient for [4Fe-4S] incorporation. The fourth ligand can vary; for example, in radical SAM enzymes, when SAM is present it is the fourth ligand (Broderick et al., Chem. Rev. 114: 4229 (2014)). Similarly to activated aconitase and other dehydratase enzymes, a water molecule (or hydroxide ion) completes the primary coordination sphere of the cluster in BMC-T1-S55C (FIG. 3B). Therefore, the [4Fe-4S] cluster of BMC-T1-S55C can be considered a hybrid between clusters found in low-potential bacterial ferredoxins (redox and spectroscopic characteristics) and those found in different classes of enzymes (architecture of the cluster).

A modification of such a BMC-T1 structure involving substitution of serine at position 56 with a cysteine (S56C) was made in the BMC-T1 gene using the QuikChange Lightning site-directed mutagenesis kit (Agilent Technologies). An amino acid sequence for such a S56C-modified BMC-T1 (BMC-T1-S56C) protein is as follows (SEQ ID NO:4).

  1 MDHAPERFDA TPPAGEPDRP  ALGVLELTSI ARGITVADAA  41 LKRAPSLLLM

LMMRGQVAEV EESMIAAREI  81 AGAGSGALLD ELELPYAHEQ LWRFLDAPVV ADAWEEDTES 121 VIIVETATVC AAIDSADAAL  KTAPVVLRDM RLAIGIAGKA 161 FFTLTGELAD VEAAAEVVRE  RCGARLLELA CIARPVDELR 181 GRLFF A modification of such a BMC-T1 structure involving substitutions of serine residues at positions 55 and 56 with a cysteine (S55C/S56C) were made in the BMC-T1 gene using the QuikChange Lightning site-directed mutagenesis kit (Agilent Technologies). An amino acid sequence for such a S55C/S56C-modified BMC-T1 (BMC-T1-S55C/S56C) protein is as follows (SEQ ID NO:5).

  1 MDHAPERFDA TPPAGEPDRP  ALGVLELTSI ARGITVADAA  41 LKRAPSLLLM

LMMRGQVAEV EESMIAAREI  81 AGAGSGALLD ELELPYAHEQ LWRFLDAPVV ADAWEEDTES 121 VIIVETATVC AAIDSADAAL  KTAPVVLRDM RLAIGIAGKA 161 FFTLTGELAD VEAAAEVVRE RCGARLLELA CIARPVDELR 181 GRLFF

A modification of such a BMC-T1 structure involving substitutions of serine at position 55 with a cysteine (S55C) and isoleucine at position 154 with a phenylalanine (I154F) were made in the BMC-T1 gene using the QuikChange Lightning site-directed mutagenesis kit (Agilent Technologies). An amino acid sequence for such a S55C/I154F-modified BMC-T1 (BMC-T1-S55C/I154F) protein is as follows (SEQ ID NO:6).

  1 MDHAPERFDA TPPAGEPDRP  ALGVLELTSI ARGITVADAA  41 LKRAPSLLLM 

LMMRGQVAEV EESMIAAREI  81 AGAGSGALLD  ELELPYAHEQ LWRFLDAPVV ADAWEEDTES 121 VIIVETATVC AAIDSADAAL  KTAPVVLRDM

161 FFTLTGELAD VEAAAEVVRE  RCGARLLELA CIARPVDELR 181  GRLFF

A modification of such a BMC-T1 structure involving substitutions of serine at position 56 with a cysteine (S56C) and isoleucine at position 154 with a phenylalanine (I154F) were made in the BMC-T1 gene using the QuikChange Lightning site-directed mutagenesis kit (Agilent Technologies). An amino acid sequence for such a S56C/I154F-modified BMC-T1 (BMC-T1-S56C/I154F) protein is as follows (SEQ ID NO:7).

  1 MDHAPERFDA TPPAGEPDRP  ALGVLELTSI ARGITVADAA  41 LKRAPSLLLM

LMMRGQVAEV EESMIAAREI  81 AGAGSGALLD ELELPYAHEQ LWRFLDAPVV ADAWEEDTES 121 VIIVETATVC AAIDSADAAL  KTAPVVLRDM

161 FFTLTGELAD VEAAAEVVRE  RCGARLLELA CIARPVDELR 181 GRLFF

A modification of such a BMC-T1 structure involving substitutions of serine at positions 55 and 56 with a cysteine (S55C/S56C) and isoleucine at position 154 with a phenylalanine (I154F) were made in the BMC-T1 gene using the QuikChange Lightning site-directed mutagenesis kit (Agilent Technologies). An amino acid sequence for such a S55C/S56C/I154F-modified BMC-T1 (BMC-T1-S55C/S56C/I154F) protein is as follows (SEQ ID NO:8).

  1 MDHAPERFDA TPPAGEPDRP  ALGVLELTSI ARGITVADAA  41 LKPAPSLLLM

  LMMRGQVAEV EESMIAAREI  81 AGAGSGALLD ELELPYAHEQ  LWRFLDAPVV ADAWEEDTES 121 VIIVETATVC AAIDSADAAL  KTAPVVLRDM

161 FFTLTGELAD VEAAAEVVRE  RCGARLLELA CIARPVDELR 181 GRLFF

These mutations have been designed to create an alternative [4Fe-4S] cluster binding site or to alter the environment of the cluster, with the objective of fine-tuning its reduction potential. More specifically, the S55C and S56C mutations provide [4F-4S] cluster binding sites located in the concave and the convex face of BMC-T1, respectively (FIG. 7). The presence of a double set of cysteine residues (S55C/S56C) as well as the mutation of an adjacent isoleucine residue to a phenylalanine residue modifies the environment of the cluster and its properties.

To form its shell, a bacterial microcompartment assembles from several BMC-T subunits (e.g., three BMC-T subunits), several BMC-P subunits (e.g., three BMC-P subunits) and at least one BMC-H subunit.

An example, of an amino acid sequence for a Haliangium ochraceum BMC-H (Hoch_5815) shell subunit is shown below as SEQ ID NO:9.

1 MADALGMIEV RGFVGMVEAA DAMVKAAKVE LIGYEKTGGG 41 YVTAVVRGDV AAVKAATEAG QRAAERVGEV VAVHVIPRPH 81 VNVDAALPLG RTPGMDKSA A nucleotide sequence for this Haliangium ochraceum BMC-H (Hoch_5815) shell protein is shown below as SEQ ID NO:10.

1 ATGGCGGACG CACTGGGTAT GATTGAAGTT CGTGGTTTTG 41 TTGGTATGGT GGAAGCGGCG GATGCTATGG TGAAAGCGGC 81 TAAAGTTGAA CTGATTGGTT ATGAAAAAAC CGGCGGTGGC 121 TACGTGACGG CAGTGGTTCG TGGTGATGTC GCAGCAGTTA 161 AGGCAGCTAC CGAAGCCGGT CAGCGTGCAG CAGAACGTGT 201 TGGTGAAGTC GTGGCAGTTC ATGTCATCCC GCGTCCGCAC 241 GTGAACGTTG ATGCAGCTCT GCCGCTGGGT CGTACGCCGG 321 GTATGGACAA AAGCGCGTAA

An example of an amino acid sequence for a Haliangium ochraceum BMC-T3 (Hoch_3341) shell protein is shown below as SEQ ID NO: 11.

1 MELRAYTVLD ALQPQLVAFL QTVSTGFMPM EQQASVLVEI 41 APGIAVNQLT DAALKATRCQ PGLQIVERAY GLIEMHDDDQ 81 GQVRAAGDAM LAHLGAREAD RLAPRVVSSQ IITGIDGHQS 121 QLINRMRHGD MIQAGQTLYI LEVHPAGYAA LAANEAEKAA 161 PIKLLEVVTF GAFGRLWLGG GEAEIAEAAR AAEGALAGLS 201 GRDNRG A nucleotide segment encoding the Haliangium ochraceum BMC-T3 (Hoch_3341) shell protein can, for example, have the following nucleotide sequence (SEQ ID NO:12).

1 ATGGAACTGC GTGCTTATAC GGTCCTGGAT GCCCTGCAGC 41 CGCAACTGGT CGCCTTTCTG CAAACGGTGT CAACGGGTTT 81 CATGCCGATG GAACAGCAAG CGAGCGTTCT GGTCGAAATT 121 GCACCGGGTA TCGCTGTCAA CCAGCTGACC GACGCAGCAC 161 TGAAAGCAAC GCGTTGCCAG CCGGGTCTGC AAATTGTGGA 201 ACGTGCGTAT GGCCTGATCG AAATGCATGA TGACGATCAG 241 GGTCAAGTTC GTGCAGCTGG TGACGCAATG CTGGCACACC 281 TGGGTGCACG TGAAGCTGAT CGTCTGGCAC CGCGTGTGGT 321 TAGCTCTCAG ATTATCACCG GTATTGACGG CCATCAGAGT 361 CAACTGATCA ACCGTATGCG CCACGGTGAT ATGATTCAGG 401 CAGGCCAAAC GCTGTATATC CTGGAAGTTC ATCCGGCAGG 441 TTACGCAGCA CTGGCAGCTA ATGAAGCCGA AAAAGCGGCC 481 CCGATTAAGC TGCTGGAAGT CGTGACCTTT GGTGCATTCG 521 GTCGTCTGTG GCTGGGTGGT GGTGAAGCAG AAATCGCAGA 561 AGCAGCTCGT GCGGCAGAAG GTGCACTGGC TGGTCTGTCC 601 GGCCGTGATA ATCGCGGCTA A

An example of another amino acid sequence for a Haliangium ochraceum BMC-T2 (HOCH_5816) shell protein is shown below as SEQ ID NO:13.

1 MSITLRTYIF LDALQPQLAT FIGKTARGFL PVPGQASLWV 41 EIAPGIAINR VTDAALKATK VQPAVQVVER AYGLLEVHHF 81 DQGEVLAAGS TILDKLEVRE EGRLKPQVMT HQIIRAVEAY 121 QTQIINRNSQ GMMILPGESL FILETQPAGY AVLAANEAEK 161 AANVHLVNVT PYGAFGRLYL AGSEAEIDAA AEAAEAAIRS 201 VSGVAQESFR DR A nucleotide segment encoding the Haliangium ochraceum BMC-T2 (HOCH_5816) shell protein can, for example, have the following nucleotide sequence (SEQ ID NO:14).

1 ATGTCAATCA CCCTGCGCAC CTATATCTTT CTGGACGCCC 41 TGCAACCGCA ACTGGCAACC TTCATCGGCA AAACGGCTCG 81 TGGCTTCCTG CCGGTCCCGG GTCAGGCAAG CCTGTGGGTG 121 GAAATTGCTC CGGGTATTGC GATCAACCGT GTGACCGATG 161 CGGCCCTGAA AGCTACGAAG GTGCAGCCGG CGGTTCAAGT 201 GGTTGAACGC GCGTATGGCC TGCTGGAAGT TCATCACTTC 241 GATCAGGGCG AAGTCCTGGC AGCTGGTAGT ACCATCCTGG 281 ACAAACTGGA AGTTCGTGAA GAAGGTCGCC TGAAGCCGCA 321 GGTGATGACC CATCAAATTA TCCGTGCTGT TGAAGCGTAT 361 CAGACGCAAA TTATCAACCG CAATAGTCAG GGCATGATGA 401 TTCTGCCGGG TGAATCCCTG TTTATCCTGG AAACCCAACC 441 GGCAGGTTAC GCAGTCCTGG CAGCCAATGA AGCCGAAAAA 481 GCAGCTAACG TTCACCTGGT CAATGTGACG CCGTATGGCG 521 CATTCGGTCG TCTGTACCTG GCCGGCTCAG AAGCAGAAAT 561 TGATGCGGCC GCAGAAGCTG CGGAAGCCGC AATCCGCAGC 601 GTTTCTGGTG TCGCGCAGGA ATCGTTTCGT GACCGCTAA

An example, of an amino acid sequence for a Haliangium ochraceum BMC-P (Hoch_4425) shell protein is shown below as SEQ ID NO:15.

1 MYLGRVIGTV VAERKVAGLE GAKLLLVQPL DDALSPVGGV 41 QAAVDTVQAG PDDLVYLVGS REAALALTPS FVPVDAAIVG 81 IVDDVHAPER AS A nucleotide segment encoding the Haliangium ochraceum BMC-P (Hoch_4425) shell protein can, for example, have the following nucleotide sequence (SEQ ID NO: 16).

1 ATGTATCTGG GTCGTGTGAT TGGTACCGTG GTGGCTGAAC 41 GCAAAGTGGC GGGTCTGGAA GGCGCAAAAC TGCTGCTGGT 81 GCAACCGCTG GATGACGCAC TGAGTCCGGT CGGTGGTGTG 121 CAGGCAGCAG TTGATACCGT CCAAGCAGGT CCGGATGACC 161 TGGTGTATCT GGTTGGTAGC CGTGAAGCAG CTCTGGCGCT 201 GACGCCGTCT TTTGTGCCGG TTGATGCGGC CATTGTCGGC 241 ATCGTTGATG ACGTGCATGC ACCGGAACGC GCTAGCTAA

An example of another amino acid sequence for a Haliangium ochraceum BMC-P (Hoch_4426) shell protein is shown below as SEQ ID NO:17.

1 MRLCRVLGSV VATVKHPVYN GLPLMIVQPL DDAGRDAGAS 41 FLAVDNVQSG PGDRVLVLTE GGGVRQILAL GDQVPIRSLI 81 VGVVDAVDGV AATGVDDAGG AADSAAAAKS VRADELPADA 121 SAAGRGE A nucleotide segment encoding the Haliangium ochraceum BMC-P (Hoch_4426) shell protein can, for example, have the following nucleotide sequence (SEQ ID NO: 18).

1 ATGCGTCTGT GTCGTGTTCT GGGCTCCGTC GTCGCCACCG 41 TCAAGCACCC GGTCTACAAT GGTCTGCCGC TGATGATCGT 81 TCAACCGCTG GATGACGCAG GTCGTGATGC AGGCGCTAGT 121 TTTCTGGCTG TTGATAACGT CCAGTCCGGT CCGGGTGACC 161 GTGTCCTGGT GCTGACCGAA GGTGGTGGTG TGCGTCAGAT 201 TCTGGCACTG GGTGATCAAG TCCCGATTCG CAGCCTGATC 241 GTGGGCGTGG TTGATGCAGT GGACGGTGTT GCAGCAACGG 281 GTGTTGATGA CGCAGGTGGT GCAGCTGATA GCGCAGCAGC 321 AGCTAAATCT GTCCGTGCAG ATGAACTGCC GGCAGACGCA 361 AGCGCGGCCG GTCGCGGCGA ATAA

An example of another amino acid sequence for a Haliangium ochraceum BMC-P (Hoch_5814) shell protein is shown below as SEQ ID NO:19.

1 MVLGKVVGTV VASRKEPRIE GLSLLLVRAC DPDGTPTGGA 41 VVCADAVGAG VGEVVLYASG SSARQTEVTN NRPVDATIMA 81 IVDLVEMGGD VRFRKD A nucleotide segment encoding the Haliangium ochraceum BMC-P (Hoch_5814) shell protein can, for example, have the following nucleotide sequence (SEQ ID NO:20).

1 ATGGTCCTGG GTAAAGTCGT GGGTACGGTG GTGGCGAGCC 41 GCAAAGAACC GCGCATTGAA GGTCTGAGCC TGCTGCTGGT 81 CCGTGCCTGC GATCCGGACG GTACCCCGAC GGGTGGTGCA 121 GTGGTTTGTG CAGATGCAGT GGGTGCAGGT GTTGGTGAAG 161 TCGTGCTGTA TGCGAGTGGC AGCTCTGCCC GTCAGACCGA 201 AGTCACGAAC AATCGCCCGG TTGATGCAAC CATTATGGCT 241 ATCGTTGACC TGGTCGAAAT GGGCGGTGAT GTGCGTTTTC 281 GCAAAGACTAA

A synthetic operon was constructed with ribosomal binding site sequences from the Community RBS Collection of the Registry of Standard Biological Parts (partsregistry.org) as described by Lassila et al. (J. Mol. Biol. 426: 2217 (2014)):

(SEQ ID NO: 21) For BMC-H: TCTAGAGAAAGAGGAGAAATACTAGATG (SEQ ID NO: 22) For BMC-T: TCTAGAGATTAAAGAGGAGAAATACTAGATG (SEQ ID NO: 23) For BMC-P: TCTAGAGTCACACAGGAAACCTACTAGATG The full sequence of this synthetic H. ochraceum operon has the following sequence (SEQ ID NO:24) with sequences that separate the different microcompartment subunits identified in bold and with underlining.

ATGGCGGACGCACTGGGTATGATTGAAGTTCGTGG TTTTGTTGGTATGGTGGAAGCGGCGGATGCTATGG TGAAAGCGGCTAAAGTTGAACTGATTGGTTATGAA AAAACCGGCGGTGGCTACGTGACGGCAGTGGTTCG TGGTGATGTCGCAGCAGTTAAGGCAGCTACCGAAG CCGGTCAGCGTGCAGCAGAACGTGTTGGTGAAGTC GTGGCAGTTCATGTCATCCCGCGTCCGCACGTGAA CGTTGATGCAGCTCTGCCGCTGGGTCGTACGCCGG GTATGGACAAAAGCGCGTAA

ATGGACCACGCTCCGGAACGCTTTGATGCGACCCC GCCGGCAGGTGAACCGGACCGCCCGGCACTGGGTG TGCTGGAACTGACCTCAATTGCTCGTGGTATCACC GTTGCGGATGCGGCCCTGAAACGTGCACCGAGTCT GCTGCTGATGTCCCGCCCGGTCAGCTCTGGCAAGC ATCTGCTGATGATGCGTGGCCAGGTGGCAGAAGTT GAAGAATCAATGATTGCAGCTCGCGAAATCGCTGG TGCAGGTTCGGGTGCTCTGCTGGATGAACTGGAAC TGCCGTATGCGCACGGAACAACTGTGGCGCTTTCT GGACGCACCGGTGGTTGCAGATGCATGGGAAAAGA CACCGAAAGCGTCATTATCGTGGAAACCGCGACGG TGTGCGCGGCCATTGATAGTGCCGACGCAGCTCTG AAAACGGCACCGGTCGTGCTGCGTGATATGCGCCT GGCCATTGGTATCGCTGGCAAGGCGTTTTTCACCC TGACGGGTGAACTGGCAGACGTGGAAGCGGCCGCA GAAGTTGTCCGTGAACGTTGCGGTGCACGTCTGCT GGAACTGGCATGTATCGCACGCCCGGTTGATGAAC TGCGTGGCCGCCTGTTTTTCTAA

ATGGAACTGCGTGCTTATACGGTCCTGGATGCCCT GCAGCCGCAACTGGTCGCCTTTCTGCAAACGGTGT CAACGGGTTTCATGCCGATGGAACAGCAAGCGAGC GTTCTGGTCGAAATTGCACCGGGTATCGCTGTCAA CCAGCTGACCGACGCAGCACTGAAAGCAACGCGTT GCCAGCCGGGTCTGCAAATTGTGGAACGTGCGTAT GGCCTGATCGAAATGCATGATGACGATCAGGGTCA AGTTCGTGCAGCTGGTGACGCAATGCTGGCACACC TGGGTGCACGTGAAGCTGATCGTCTGGCACCGCGT GTGGTTAGCTCTCAGATTATCACCGGTATTGACGG CCATCAGAGTCAACTGATCAACCGTATGCGCCACG GTGATATGATTCAGGCAGGCCAAACGCTGTATATC CTGGAAGTTCATCCGGCAGGTTACGCAGCACTGGC AGCTAATGAAGCCGAAAAAGCGGCCCCGATTAAGC TGCTGGAAGTCGTGACCTTTGGTGCATTCGGTCGT CTGTGGCTGGGTGGTGGTGAAGCAGAAATCGCAGA AGCAGCTCGTGCGGCAGAAGGTGCACTGGCTGGTC TGTCCGGCCGTGATAATCGCGGCTAA

ATGTCAATCACCCTGCGCACCTATATCTTTCTGGA CGCCCTGCAACCGCAACTGGCAACCTTCATCGGCA AAACGGCTCGTGGCTTCCTGCCGGTCCCGGGTCAG GCAAGCCTGTGGGTGGAAATTGCTCCGGGTATTGC GATCAACCGTGTGACCGATGCGGCCCTGAAAGCTA CGAAGGTGCAGCCGGCGGTTCAAGTGGTTGAACGC GCGTATGGCCTGCTGGAAGTTCATCACTTCGATCA GGGCGAAGTCCTGGCAGCTGGTAGTACCATCCTGG ACAAACTGGAAGTTCGTGAAGAAGGTCGCCTGAAG CCGCAGGTGATGACCCATCAAATTATCCGTGCTGT TGAAGCGTATCAGACGCAAATTATCAACCGCAATA GTCAGGGCATGATGATTCTGCCGGGTGAATCCCTG TTTATCCTGGAAACCCAACCGGCAGGTTACGCAGT CCTGGCAGCCAATGAAGCCGAAAAAGCAGCTAACG TTCACCTGGTCAATGTGACGCCGTATGGCGCATTC GGTCGTCTGTACCTGGCCGGCTCAGAAGCAGAAAT TGATGCGGCCGCAGAAGCTGCGGAAGCCGCAATCC GCAGCGTTTCTGGTGTCGCGCAGGAATCGTTTCGT GACCGCTAA

ATGTATCTGGGTCGTGTGATTGGTACCGTGGTGGC TGAACGCAAAGTGGCGGGTCTGGAAGGCGCAAAAC TGCTGCTGGTGCAACCGCTGGATGACGCACTGAGT CCGGTCGGTGGTGTGCAGGCAGCAGTTGATACCGT CCAAGCAGGTCCGGATGACCTGGTGTATCTGGTTG GTAGCCGTGAAGCAGCTCTGGCGCTGACGCCGTCT TTTGTGCCGGTTGATGCGGCCATTGTCGGCATCGT TGATGACGTGCATGCACCGGAACGCGCTAGCTAA

ATGCGTCTGTGTCGTGTTCTGGGCTCCGTCGTCGC CACCGTCAAGCACCCGGTCTACAATGGTCTGCCGC TGATGATCGTTCAACCGCTGGATGACGCAGGTCGT GATGCAGGCGCTAGTTTTCTGGCTGTTGATAACGT CCAGTCCGGTCCGGGTGACCGTGTCCTGGTGCTGA CCGAAGGTGGTGGTGTGCGTCAGATTCTGGCACTG GGTGATCAAGTCCCGATTCGCAGCCTGATCGTGGG CGTGGTTGATGCAGTGGACGGTGTTGCAGCAACGG GTGTTGATGACGCAGGTGGTGCAGCTGATAGCGCA GCAGCAGCTAAATCTGTCCGTGCAGATGAACTGCC GGCAGACGCAAGCGCGGCCGGTCGCGGCGAATAA

ATGGTCCTGGGTAAAGTCGTGGGTACGGTGGTGGC GAGCCGCAAAGAACCGCGCATTGAAGGTCTGAGCC TGCTGCTGGTCCGTGCCTGCGATCCGGACGGTACC CCGACGGGTGGTGCAGTGGTTTGTGCAGATGCAGT GGGTGCAGGTGTTGGTGAAGTCGTGCTGTATGCGA GTGGCAGCTCTGCCCGTCAGACCGAAGTCACGAAC AATCGCCCGGTTGATGCAACCATTATGGCTATCGT TGACCTGGTCGAAATGGGCGGTGATGTGCGTTTTC GCAAAGACTAA

The microcompartment shell subunits can have sequence variations. For example, the bacterial microcompartment subunits used to generate the microcompartments can have at least 30%, at least 40%, at least 50%, 60%, at least 70%, or at least 75%, or at least 80%, or at least 85%, or at least 90%, or at least 95%, or at least 97% sequence identity to any of SEQ ID NO: 1-20 or 24, especially in the aligned region of the PFAM00936 domain.

For example, a related BMC sequence is available from Deltaproteobacteria bacterium CG2_30_63_29 (SEQ ID NO:36) has at least 42% sequence identity to SEQ ID NO: 1, as illustrated below, where the amino acids at positions corresponding to the 55, 56 and 154 positions of the SEQ ID NO:1 protein are highlighted in the Deltaproteobacteria bacterium protein. These amino acids can be modified. For example, the Deltaproteobacteria bacterium can have cysteines at the positions corresponding to positions 55 and/or 56; and the Deltaproteobacteria bacterium protein can have phenylalanine at the position corresponding to position 154 of the SEQ ID NO:1 protein.

SEQ:  1  21

SEQ: 18  18

SEQ:  1  81 AGAGSGALLDELELPYAHEQLW----RFLDAPVVADAWEEDTESVIIVETATVCAAIDS **     **  * *** * ***     *   *                *  **  **  SEQ: 18  78 AC---NQLLADLFLPYCHPQLWDGLFQKFKRTPI---------DALGLFECHTVVDAILG SEQ:  1 136

SEQ: 18 126

SEQ:  1 195 PVDEL 199 * *  SEQ: 18 186 PHDDM 190 The Deltaproteobacteria bacterium protein is available as accession number OIP31652.1 from the NCBI database, and the sequence of this protein is shown below as SEQ ID NO: 36, with the amino acids that can be modified highlighted.

  1  MPNDLRHIGN GDSAPSEALG VIELGTIIRG YRVLDAMVKR  41  SPITVRAAYP

EGGVAEVDEA MQAGRPAAGN  81  OLLADLFLPY CHPQLWDGLF QKFKRIPIDA LGLFECHTVV 121  DAILGADVAL KAAEVNLAAL

YFVVSGELFD 161  AEAAIEAALD RIDEPRIIEH DVLCAPHDDM TLELLGLQTV 201  HEKY

Another example of a related BMC sequence is available from Hyalangium minutum that has at least 49% sequence identity to SEQ ID NO: 1, as illustrated below, where the amino acids at positions corresponding to the 55, 56 and 154 positions of the SEQ ID NO: 1 protein are highlighted in the Hyalangium minutum protein. These amino acids can be modified. For example, the Hyalangium minutum can have cysteines at the positions corresponding to positions 55 and/or 56; and the Hyalangium minutum protein can have phenylalanine at the position corresponding to position 154 of the SEQ ID NO:1 protein.

SEQ   1 20

SEQ  37 10

SEQ   1 80 IAGAGSGALLDELELPYAHEQLWRFLDAPVVADAWEEDTESVIIVETATVCAAIDSADAA   +AG   LLD+L LP A + L   L             ESV IVET TV AA+  AD A SEQ  37 70 VAGR---TLLDKLLLPMAADGLVAGLQGRFPGTFG---ESVGIVETHTVAAALLCADTA SEQ   1 140

SEQ  37 123

SEQ   1 199 LRGRLF 204 **** SEQ  37 183 LRGRVL 188 The Hyalangium minutum protein is available as accession number KFE69389.1 from the NCBI database, and the sequence of this protein is shown below as SEQ ID NO: 37, with the amino acids that can be modified highlighted.

  1  MSDPLPLPGP ALALLELDSI ARGYVVADAV VKRAPVTLAM  41 

LLFSGGVAEV QESFQEGLEV AGRTLLDKLL  61  LPMAADGLVA GLQGRFPGTF GESVGIVETH TVAAALLCAD 121  TALKRAEVVL

GKGVFVLAGE LHMVEAALEG 161  AAAAVEPHLL LTTEIIQRPS PELRGRVL

Such alignments illustrate that a variety of BMC proteins can be modified to have cysteines at the positions corresponding to positions 55 and/or 56 of the SEQ ID NO: 1 protein; and/or a phenylalanine at the position corresponding to position 154 of the SEQ ID NO: 1 protein. These modified BMC proteins can also incorporate iron (e.g., [4Fe-4S] clusters) in the manner illustrated herein.

Additional Components

Bacterial microcompartments (BMCs) are polyhedral organelles (typically 40-200 nm in diameter) consisting of a proteinaceous shell that can enclose a multi-enzyme core (recently reviewed by Kerfeld & Erbilgin, Trends Microbiol. 2015, 23: 22 (2015); and Bobik et al., Mol. Microbiol 98: 193 (2015)). While all types of BMCs share an architecturally similar shell, the encapsulated enzymes can vary, contributing to the remarkable functional and phylogenetic diversity of BMCs (Axen et al., PLoS Comput. Biol. 10: e1003898 (2014)).

Bacterial microcompartments can serve as nanobiocatalytic sites and reactors in vivo or in vitro. The modified bacterial microcompartments serving as nanobiocatalytic sites can include one or more enzymes within them that can catalyze various reactions. The enzymes can naturally be encapsulated within the microcompartments, or the enzymes can be tethered to one or more of the subunits of the microcompartments. Examples of enzymes that can be encapsulated or tethered within the modified microcompartments can include nitrogenases, enzymes of the methylerythritol 4-phosphate (MEP) pathway MEP pathway (e.g., IspG and IspH), and/or enzymes that can catalyze the conversion of NAD/NADP.

In some cases, the modified bacterial microcompartments can include one or more nitrogenases, for example, to improve nitrogen fixation. Nitrogenases can reduce nitrogen (N₂) to NH₃ via nitrogen fixation and are found in certain bacteria (such as cyanobacteria). Nitrogenase typically consists of two proteins that work in tandem: the iron (Fe) protein and the molybdenum-iron (MoFe) protein. During the catalytic reduction of nitrogen, the electrons are transferred from the Fe-protein to the MoFe-protein.

The iron protein component of nitrogenase accepts the electrons, typically from a flavodoxin or a ferredoxin, and transfers them further to the MoFe-protein. This electron transfer can be enabled in some cases by simultaneous hydrolysis of ATP to ADP.

An example of a sequence for a nitrogenase Fe-protein from Rhizobium phaseoli is available from the UniProt database as accession number A0A192TMU2, and provided below as SEQ ID NO:26.

        10         20         30         40 MSDLRQIAFY GKGGIGKSTT SQNTLAALVD LGQKILIVGC         50         60         70         80 DPKADSTRLI LNAKAQDTVL HLAAQEGSVE DLELEDVLKA         90        100        110        120 GYKGIKCVES GGPEPGVGCA GRGVITSINF LEENGAYDDV        130        140        150        160 DYVSYDVLGD VVCGGFAMPI RENKAQEIYI VMSGEMMALY        170        180        190        200 AANNIAKGIL KYAHSGGVRL GGLICNERQT DRELDLSEAL        210        220        230        240 AARLNSKLIH FVPRDNIVQH AELRKMTVIQ YAPDSKQAGE        250        260        270        280 YRALAEKIHA NSGQGTIPTP ITMEELEDML LDFGIMKSDE        290 QMLAELQAKE SAVVAAQ

An example of a sequence for a nitrogenase Fe-protein from Bacteroidales bacterium Barb6XT is available from the UniProt database as accession number A0A180F7Y, and provided below as SEQ ID NO:27.

        10         20         30         40 MSKKIKQIAV YGKGGIGKST TTSNISAALV EAGHKVLQFG         50         60         70         80 CDPKSDSTNT LRDGKYIPTV LDLLREKPKV DAHEAIFQGF         90        100        110        120 KGVYCVEAGG PAPGVGCAGR GIITAVELLK SQHIFEELDL        130        140        150        160 DYVIYDVLGD VVCGGFAVPI REGIAEHVFT VSSSDFMSIY        170        180        190        200 AANNLMKGIK KYSNSGGALF GGIIANSINS SYQRAIIDDF        210        220        230        240 TQQTGTQVVE YVPRSITVIQ AELSGRTTIE AQPISVQADI        250        260        270        280 YRSLAKKIHE HTESRVPTPL EIDALREWSA RWADQLLATE        290 AGEVRGTOAG I

A comparison of the sequences of the Rhizobium phaseoli nitrogenase Fe-protein with SEQ ID NO:26 and the Bacteroidales bacterium Barb6XT nitrogenase Fe-protein with SEQ ID NO:27 is shown below.

46.1% identity in 267 residues overlap; Score: 603.0; Gap frequency: 2.2% Rhizobium 4 LRQIAFYGKGGIGKSTTSQNTLAALVDLGQKILIVGCDPKADSTRLILNAKAQDTVLHLA Bacteroid 5 IKQIAVYGKGGIGKSTTTSNISAALVEAGHKVLQFGCDPKSDSTNTLRDGKYIPTVLDLL   *** ***********  *  ****  * * *  ***** ***      *   *** * Rhizobium 64 AQEGSVEDLELEDVLKAGYKGIKCVESGGPEPGVGCAGRGVITSINFLEENGAYD--DVD Bacteroid 65 REKPKVD---AHEAIFQGFKGVYCVEAGGPAPGVGCAGRGIITAVELLKSQHIFEELDLD      *           * **  *** *** ********* **    *         * * Rhizobium 122 YVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMALYAANNIAKGILKYAHSGGVRLG Bacteroid 122 YVIYDVLGDVVCGGFAVPIREGIAEHVFTVSSSDFMSIYAANNLMKGIKKYSNSGGALFG ** ************* ****  *     * *   *  *****  *** **  ***   * Rhizobium 182 GLICNERQTDRELDLSEALAARLNSKLIHFVPRDNIVQHAELRKMTVIQYAPDSKQAGEY Bacteroid 182 GIIANSINSSYQRAIIDDFTQQTGTQVVEYVPRSITVTQAELSGRTTIEAQPISVQADIY * * *                         ***   *  ***   * *   * * **  * Rhizobium 242 RALAEKIHANSGQGTIPTPITMEELED Bacteroid 242 RSLAKKIHEHT-ESRVPTPLEIDALRE * ** ***        ***     *

Such a comparison of amino acid sequences illustrates what are the conserved and non-conserved regions of these proteins, allowing those of skill in the art to identity regions or amino acids that can be changed without adversely affecting the structure and activities of the proteins. Such a comparison can also illuminate which amino acids may serve as linkage sites for tethering the proteins to one or more microcompartment subunits.

An example of a sequence for a nitrogenase molybdenum-iron (MoFe) protein from Gluconacetobacter diazotrophicus is available from the UniProt database as accession number A9H5W8, and provided below as SEQ ID NO:28.

        10         20         30         40 MPQNVDKILD HAPLFREPEY QEMLAGKAKL ENMPPADKVV         50         60         70         80 EIADWTKSWE YREKNFARES LSVNPAKACQ PLGAVFVASG         90        100        110        120 FERTMSFVHG SQGCVAYYRS HLSRHFKEPS SAVSSSMTED        130        140        150        160 AAVFGGLNNM VDGLANTYKL YDPKMIAVST TCMAEVIGDD        170        180        190        200 LHAFIQTAKG KGSVPEEFDV PFAHTPAFVG SHVTGYDNML        210        220        230        240 KGILEHFWKG RTPVPNRSVN IIPGFDGFAV GNNRELKRIL        250        260        270        280 GMMGVQYTIL SDVSDQFDTP SDGEYRMYDG GTKIEAARDA        290        300        310        320 VNADYTISLQ EYCTPKTLEY CQSFGQKTAS FHYPLGIGAT        330        340        350        360 DDLLQKLSEI SGKPVPQELE MERGRLVDAL ADSQAYLHGK        370        380        390        400 TYAIYGDPDF VYGMARFILE TGGEPKHCLA TNGSKAWEAQ        410        420        430        440 MQELFDSSPF GVGCKAWGGK DLWHMRSLLA TEKVDLLIGN        450        460        470        480 SYGKYLERDT DTPLIRLMFP IFDRHHHHRF PVWGYQGALR        490        500        510 VLVTLLDKIF DKLDDDTIQA GVTDYSFDLT R

An example of a sequence for a nitrogenase molybdenum-iron (MoFe) protein from Bacteroidales bacterium Barb6XT is available from the UniProt database as accession number A0A180F7W2 and provided below as SEQ ID NO:29.

        10         20         30         40 MLLRHTTAQE IERKALTINP AKTCQPVGAM YAALGLHGCL         50         60         70         80 PHSHGSQGCC SYHRSALTRH FKEPVMAATS SFSEGSSVFG         90        100        110        120 GSANLVTAIE TIFTVYNPDV VAVHTTCLSE TIGDDLTQIV        130        140        150        160 SKAHEDGLVP EGKKVIYCNT PSYVGTHVTG YSNQVAAFVK        170        180        190        200 FFSTATPKKK NVVNLVAGWM EPSDMREIKR LAQEMEARII        210        220        230        240 LFPDMSGVLD APLTGKFEMY PKGGITQAQL IATGDSKFTI        250        260        270        280 GLGAYTTEDA CVKLENKCKV KFEVVEIPIG LKATDRFITS        290        300        310        320 LSRHANVPVP DSITEERGRL VDLIADNSKY FYGKRVALFG        330        340        350        360 DPDTLIPLTE FLLTLDMKPV YIVTGTPGKH FDESMKTLLS        370        380        390        400 EKVPEAKYKS GPNADMFQLH QWIKQEPVDL LIGNTYCKYI        410        420        430        440 ARDENIPFVR LGFPIVDRAG HNYFPNTGYV GATNLVIKIL        450        460 EKELDHLDRN CPDEKVEWQL

A comparison of the sequences of the Gluconacetobacter diazotrophicus nitrogenase molybdenum-iron (MoFe) protein with SEQ ID NO:28 and the Bacteroidales bacterium Barb6XT nitrogenase molybdenum-iron (MoFe) protein with SEQ ID NO:29 is shown below.

37.4% identity in 439 residues overlap; Score: 765.0; Gap frequency: 1.1% Gluconace 58 RESLSVNPAKACQPLGAVFVASGFERTMSFVHGSQGCVAYYRSHLSRHFKEPSSAVSSSM Bacteroid 13 RKALTINPAKTCQPVGAMYAALGLHGCLPHSHGSQGCCSYHRSALTRHFKEPVMAATSSF *  *  **** *** **   * *        ******  * ** * ******  *  ** Gluconace 118 TEDAAVFGGLNNMVDGLANTYKLYDPKMIAVSTTCMAEVIGDDLHAFIQTAKGKGSVPEE Bacteroid 73 SEGSSVFGGSANLVTAIETIFTVYNEDVVAVHTTCLSETIGDDLTQIVSKAHEDGLVPEG  *   ****  * *         * *   ** ***  * *****      *   * *** Gluconace 178 FDVPFAHTPAFVGSHVTGYDNMLKGILEHFWKGRTPVPNRSVNIIPGFDGFAVGNNRELK Bacteroid 133 KKVIYCNTPSYVGTHVTGYSNQVAAFVK-FFSTATPKKKNVVNLVAGW--MEPSDMREIK   *    **  ** ***** *        *    **     **   *         ** * Gluconace 238 RILGMMGVQYTILSDVSDQFDTPSDGEYRMYDGGTKIEAARDAV-NADYTISLQEYCTPK Bacteroid 190 RLAQEMEARIILFPDMSGVLDAPLTGKFEMYPKGGTTQAQLIATGDSKFTIGLGAYTTED *    *        * *   * *  *   **  *    *   *      ** *  * * Gluconace 297 TLEYCQSFGQ-KTASFHYPLGIGATDDLLQKLSEISGKPVPQELEMERGRLVDALADSQA Bacteroid 250 ACVKLENKCKVKFEVVEIPIGLKATDRFITSLSRHANVPVPDSITEERGRLVDLIADNSK            *      * *  ***     **     ***     *******  ** Gluconace 356 YLHGKTYAIYGDPDFVYGYARFILETGGEPKHCLATNGSKAWEAQMQELFDSSPFGVGCK Bacteroid 310 YFYGKRVALFGDPDTLIPLTEFLLTLDMKPVYIVTGTPGKHFDESMKTLLSEKVPEAKYK *  **  *  ****       * *     *         *     *  *          * Gluconace 416 AWGGKDLWHMRSLLATEKVDLLIGNSYGKYLERDTDTPLIRLMFPIFDRHHHHRFPVWGY Bacteroid 370 SGPNADMFQLHQWIKQEPVDLLIGNTYGKYIARDENIPFVRLGFPIVDRAGHNYFPNTGY      *          * ******* ****  **   *  ** *** **  *  **  ** Gluconace 476 QGALRVLVTLLDKIFDKLD Bacteroid 430 VGATNLVIKILEKELDHLD  **       * *  * **

Such a comparison of amino acid sequences illustrates what are the conserved and non-conserved regions of these proteins, allowing those of skill in the art to identity regions or amino acids that can be changed without adversely affecting the structure and activities of the proteins. Such a comparison, combined with structural modeling, can also illuminate which amino acids may serve as linkage sites for tethering the proteins to one or more microcompartment subunits.

The modified bacterial microcompartments can also encapsulate one or more enzymes of the methylerythritol 4-phosphate (MEP) pathway MEP pathway (e.g., IspG and IspH) to improve production of the basic building blocks for the biosynthesis of terpenes. Such terpenes include numerous chemicals (more than 55,000 are known) that provide starting materials and intermediates for production of pharmaceuticals, biofuels, fragrances and more. For example, IspG and IspH are enzymes that can use the [4Fe-4S] cluster and the electrons provided for their catalytic activity. IspG and IspH are generally sensitive to oxygen and not very catalytically efficient; encapsulation protects them from oxygen and can improve their efficiency.

An example of a sequence for IspG (4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (flavodoxin)) protein from Streptomyces clavuligerus is available from the UniProt database as accession number B5GZ64 and provided below as SEQ ID NO:30.

        10         20         30         40 MTAISLGMPS VPTKLADRR SRKIQVGSVA VGGDAPVSVQ         50         60         70         80 SMTTTRTSDI GATLOQIAEL TASGCQIVRV ACPTQDDADA         90        100        110        120 LATIARKSQI PVIADIHFQP KYVFAAIDAG CAAVRVNPGN        130        140        150        160 IKQFDDKVKE IAKAASASGT PIRIGVNAGS LDARLLKKYG        170        180        190        200 KATPEALVES ALWEASLFEE HGFQDIKISV KHNDPVVMVN        210        220        230        240 AYRQLAAQCD YPLHLGVTEA GPAFQGTIKS AVAFGALLSE        250        260        270        280 GIGDTIRVSL SAPPAEEVKV GIQILESLNL RQRRLEIVSC        290        300        310        320 PSCGRAQVDV YKLADEVTAG LEGMEVPLRV AVMGCVVNGP        330        340        350        360 GEAREADLGV ASGNGKGQIF VKGEVIKTVP EAKIVETLIE        370        380 EAMKIAEEME KAGVMSGEPQ VSIG

An example of a sequence for IspG (4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (flavodoxin)) protein from Streptomyces roseus is available from the UniProt database as accession number A0A0J7AHR0 and provided below as SEQ ID NO:31.

        10         20         30         40 MTAISLGMPA VPTKLADRRV SRKIQVGSVA VGGDSQISVQ         50         60         70         80 SMTTTRTSDI GATLQQIAEL TASGCDIVRV ACPTQDDADA         90        100        110        120 LAVIAKKSQI PVIADIHFQP KYVFAAIDAG CAAVRVNPGN        130        140        150        160 IKQFDDKVKE IARAAKDAGT PIRIGVNAGS LDARLLKKYG        170        180        190        200 KATPEALVES ALWEASLFEE HGFSDIKISV KHNDPVVMVN        210        220        230        240 AYRQLAAQCE YPLHLGVTEA GPAFQGTIKS AVAFGALLSE        250        260        270        280 GIGDTIRVSL SAPPVEEVKV GIQILESLNL KPRRLEIVSC        290        300        310        320 PSCGRAQVDV YKLAEEVTAG LTGMEVPLRV AVMGCVVNGP        330        340        350        360 GEAREADLGV ASGNGKGQIF VKGEVIKTVP ESKIVETLIE        370        380 EAMKTAEQME KDGIASGEPT VAIGV

A comparison of the sequences of the Streptomyces clavuligerus IspG protein with SEQ ID NO:30 and the Streptomyces roseus IspG protein with SEQ ID NO:31 is shown below.

93.5% identity in 384 residues overlap; Score: 1809.0; Gap frequency: 0.0% clavuli 1 MTAISLGMPSVPTKLADDRVSRKIQVGSVAVGGDAPVSVQSMTTTRTSDIGATLQQIAEL roseus 1 MTAISLGMPAVPTKLADRRVSRKIQVGSVAVGGDSQISVQSMTTTRTSDIGATLQQIAEL ********* ************************   *********************** clavuli 61 TASGCQIVRVACPTQDDADALATIARKSQIPVIADIHFQPKYVFAAIDAGCAAVRVNPGN roseus 61 TASGGDIVRVACPTQDDADALAVIAKKSQIPVIADIHFQPKYVFAAIDAGCAAVRVNPGN ***** **************** ** ********************************** clavuli 121 IKQFDDKVKEIAKAASASGTPIRIGVNAGSLDARLLKKYGKATPEALVESALWEASLFEE roseus 121 IKQFDDKVKEIARAAKDAGTPIRIGVNAGSLDARLLKKYGKATPEALVESALWEASLFEE ************ **   ****************************************** clavuli 181 HGFQDIKISVKHNDPVVMVNAYRQLAAQCDYPLHLGVTEAGPAFQGTIKSAVAFGALLSE roseus 181 HGFSDIKISVKHNDPVVMVNAYRQLAAQCEYPLHLGVTEAGPAFQGTIKSAVAFGALLSE *** ************************* ****************************** clavuli 241 GIGDTIRVSLSAPPAEEVKVGIQILESINLRQRRLEIVSCPSCGRAQVDVYKLADEVTAG roseus 241 GIGDTIRVSLSAPPVEEVKVGIQILESLNLKPRRLEIVSCPSCGRAQVDVYKLAEEVTAG ************** ***************  ********************** ***** clavuli 301 LEGMEVPLRVAVMGCVVNGPGEAREADLGVASGNGEGQIFVKGEVIKTVPEAKDVETLIE roseus 301 LTGMEVPLRVAVMGCVVNGPGEAREADLGVASGNGKGQIFVKGEVIKTVPESKIVETLIE * ************************************************* ******** clavuli 361 EAMKIAEEMEKAGVMSGEPQVSIG roseus 361 EAMKIAEQMEKDGIASGEPTVAIG ******* *** *  **** * **

Such a comparison of amino acid sequences illustrates what are the conserved and non-conserved regions of these proteins, allowing those of skill in the art to identity regions or amino acids that can be changed without adversely affecting the structure and activities of the proteins. Such a comparison can also illuminate which amino acids may serve as linkage sites for tethering the proteins to one or more microcompartment subunits.

An example of a sequence for IspH (4-hydroxy-3-methylbut-2-enyl diphosphate reductase) protein from Streptomyces clavuligerus is available from the UniProt database as accession number B5GTV4 and provided below as SEQ ID NO:32.

        10         20         30         40 MLAAPRGYCA GVDRAVIAVE KALEQYGAPV YVRHEIVHNK         50         60         70         80 YVVQTLERKG AVFVDKTAEV PEGSIVMFSA HGVAPVVHEE         90        100        110        120 AARRKLATID ATCPLVTKVH KEAVRFANED YDILLIGHEG        130        140        150        160 HEEVIGTSGE APDHITLVDG PDDVDKVEVR DESKVVWLSQ        170        180        190        200 TTLSVDETME TVDRLKEKFP QLISPPSDDI CYATQNRQTA        210        220        230        240 VKQMGADADL VIVVGSKNSS NSVRLVEVAL GAGARDAHLV        250        260        270        280 DFAEEIDEAW LEGVATVGLT SGASVPEILV EGVLEWLSQR        290        300        310        320 GFQDVELVKA AEESITFSLP KELRRDLRAE AAALVERAEA        330 VAAGSASAHP GSASGA

An example of a sequence for IspH (4-hydroxy-3-methylbut-2-enyl diphosphate reductase) protein from Streptomyces roseus is available from the UniProt database as accession number A0A0J7APK8 and provided below as SEQ ID NO:33.

        10         20         30         40 MTAAAPVPAS PRVLLAAPRG YCAGVDRAVI AVEKALEQYG         50         60         70         80 APVYVRHEIV HNKYVVQTLE RKGAIFVERT EEVPEGSIVM         90        100        110        120 FSAHGVAPVV HEEAARGKLA TIDATCPLVT KVHKEAIRYA        130        140        150        160 NEDFDILLTG HEGHEEVIGT SGEAPDHITI VDGPHDVEKV        170        180        190        200 TVPDESKVVW LSQTTLSVDE TMETVDALKT KFPLLVSPPS        210        220        230        240 DDICYATSNR QAAVKVMGAD SDLVIVVGSK NSSNSIRLVE        250        260        270        280 VAKDAGARAA HLVDFASEID EAWLEGVSTV GLTSGASVPE        290        300        310        320 VLVFEVLEWL AARGYADVEI VKTAEESITF SLPKELRRDL        330 RAEAAELVAE K

A comparison of the sequences of the Streptomyces clavuligerus IspH protein with SEQ ID NO:32 and the Streptomyces roseus IspH protein with SEQ ID NO:33 is shown below.

88.6% identity in 315 residues overlap; Score: 1428.0; Gap frequency: 0.0% clavul 1 MLAAPRGYCAGVDRAVIAVEKALEQYGAPVYVRHEIVHNKYVVQTLERKGAVFVDKTAEV roseus 14 LLAAPRGYCAGVDRAVIAVEKALEQYGAPVYVRHEIVHNKYVVQTLERKGAIFVERTEEV ************************************************** **  * ** clavul 61 PEGSIVMFSAHGVAPVVHEEAARRKLATIDATCPLVTKVHVKEAVRFANEDYDILLIGHEG roseus 74 PEGSIVMFSAHGVAPVVHEEAARGYLATIDATCPLVTKVHVKEAIRYANEDFDILLIGHEG *********************** ******************** * **** ********* clavul 121 HEEVIGTSGEAPDHITLVDGPDDVDKVEVRDESKVVWLSQTTLSVDETMETVDRLKEKFP roseus 134 HEEVIGTSGEAPDHITIVDGPHDVEKVTVRDESKVVWLSQTTLSVDETMETVDALKTKFP **************** **** ** ** ************************* ** *** clavul 181 QLISPPSDDICYATQNRQTAVKQMGADADLVIVVGSKNSSNSVRLVEVALGAGARDAHLV roseus 194 LLVSPPSDDICYATSNRQAAVKVMGADSDLVIVVGSKNSSNSIRLVEVAKDAGARAAHLV  * *********** *** *** **** ************** ******  **** **** clavul 241 DFAEEIDEAWLEGVATVGLTSGASVPEILVEGVLEWLSQRGFQDVELVKAAEESTTESLP roseus 254 DFASEIDEAWLEGVSTVGLTSGASVPEVLVEEVLEWLAARGYADVEIVKTAEESITESLP *** ********** ************ *** *****  **  *** ** ********** clavul 301 KELRRDLRAEAAALV roseus 314 KELRRDLRAEAAELV ************ **

Such a comparison of amino acid sequences illustrates what are the conserved and non-conserved regions of these proteins, allowing those of skill in the art to identity regions or amino acids that can be changed without adversely affecting the structure and activities of the proteins. Such a comparison can also illuminate which amino acids may serve as linkage sites for tethering the proteins to one or more microcompartment subunits.

In another example, the modified bacterial microcompartments can also include enzymes that catalyze NAD/NADP conversions, which can transform the modified microcompartments and/or host cells that have such modified microcompartments into bio-batteries.

For example, host cells can have modified bacterial microcompartments can include NAD kinase, which catalyzes the following reaction: ATP+NAD⁺=ADP+NADP⁺. An example of a sequence for a Haliangium ochraceum NAD kinase is available from the UniProt database as accession number D0LKF9 and provided below as SEQ ID NO:34.

        10         20         30         40 MQRVGFILKP GQSSNERLLT ELATWVLELG HLPVIAAEDR         50         60         70         80 PVIQNVVIVP REHIGQEIDM AVVLGGDGTM LGASNLVADQ         90        100        110        120 GVPVLGINLG RLGFLTPFDL EDAEDAIADA LACKLRTSER        130        140        150        160 MRLAVTYTSD GEAPVTRTGL NDAVIHQGAM ARLIEVEAQL        170        180        190        200 DGDMVSLYRA DGLIIATPTG STAYNLAAGG PIIEPGQRAM        210        220        230        240 VLTPVCPHSL TNRSLVVPGS SSITIHLDRS ARGVVLTVDG        250        260        270        280 QWAHSFSPDD EIEIAAAARP LVVFKSDKRY FDILREKLHW        290        300        310 GARLDRSHEQ IDEAVGRRSG RISTRQDAVS DPDDDD

In another example, host cells can have modified bacterial microcompartments can include glycerol-3-phosphate dehydrogenase [NAD(P)+], which catalyzes the following reaction: sn-glycerol 3-phosphate+NAD(P)⁺→glycerone phosphate+NAD(P)H. An example of a sequence for a Haliangium ochraceum glycerol-3-phosphate dehydrogenase [NAD(P)+] is available from the UniProt database as accession number D0LJH5 and provided below as SEQ ID NO:35.

        10         20         30         40 MAQLSVIGAG SYGTSLALVF AKAGHSVSMW CHEAELAERM         50         60         70         80 QRTRENDIYL PGFALPPGIS VSSELAEVVD GADIVLGVTP         90        100        110        120 THAVRKVLGE AAGHLSGSAI VVNCSKGLEE GTLGRVDEIY        130        140        150        160 RDILPPHVYE RAVYLSGPTE AKELAAGLPA ALVVASRDAD        170        180        190        200 SAASVQHALS TDRLRLYTAP DVVGVLIGGA LKNVVAIAAG        210        220        230        240 MSDGMGLGLN ARAAIITRGL AELTRLGTHV GADPLTFAGL        250        260        270        280 SGMGDLVLTC SGDLSRNRQV GLALGAGKKR AEIVAEMRMV        290        300        310        320 AEGVNTTRVA RALAERLGVE APITEVMHRV LFEDLPASAA        330 LADLTGRALR SERA

Nucleotide segments encoding the subunits of the modified microcompartments and, optionally, the additional enzymes or components for providing nanobiocatalytic functions can be included in one or more expression cassettes or expression vectors. Such expression cassettes or expression vectors can be transformed into a host cell and/or integrated into a host cell's genome. When the subunits of the modified microcompartments and, optionally, the additional enzymes or components for providing nanobiocatalytic functions are inserted into the host cell's genome, the resulting host cells differ from a wild-type cell due to the inserted nucleotide segments.

An expression cassette can be employed that include nucleotide segments encoding the subunits of the modified microcompartments and, optionally, the additional enzymes or components for providing nanobiocatalytic functions, and one or more regulatory expression sequences. The one or more regulatory expression sequences may include a promoter. The one or more regulatory expression sequences may also include a 3′ untranslated region such as a termination sequence.

The promoters employed in expression cassettes or expression vectors can be linked to the relevant nucleotide segment(s) directly or alternatively be located in an appropriate position, for example in a vector such that when the relevant polypeptide is inserted the relevant promoter can act on the same. In one embodiment the promoter is located before the encoding portion of the polynucleotide on which it acts, for example a relevant promoter before each encoding portion of polynucleotide. “Before” as used herein is intended to imply that the promoter is located at the 5 prime end in relation to the encoding nucleotide segment.

Promoters regulate gene expression. Promoter regions are typically found in the flanking DNA upstream from the coding sequence in both prokaryotic and eukaryotic cells. A promoter sequence provides for regulation of transcription of the downstream gene sequence and typically includes from about 50 to about 2,000 nucleotide base pairs. Promoter sequences can also contain regulatory sequences such as enhancer sequences that can influence the level of gene expression. Some isolated promoter sequences can provide for gene expression of heterologous DNAs, that is a DNA different from the native or homologous DNA.

The nucleotide segment(s) can be operably linked to a promoter, which provides for expression of mRNA encoding the subunits of the modified microcompartments and, optionally, the additional enzymes or components for providing nanobiocatalytic functions. Nucleotide segment(s) are operably linked to the promoter when it is located downstream from the promoter, so that the promoter is configured to express a protein encoded by the nucleotide segment(s). The promoter employed is typically a promoter functional in bacteria.

In some cases the nucleotide segment(s) encoding the subunits of the modified microcompartments and, optionally, the additional enzymes or components for providing nanobiocatalytic functions are operably linked to a heterologous promoter. A heterologous promoter is a promoter that is not operably linked to the subunits of the modified microcompartments or the additional enzymes or components for providing nanobiocatalytic functions in nature.

Promoter sequences can be strong or weak, or inducible. A strong promoter provides for a high level of gene expression, whereas a weak promoter provides for a very low level of gene expression. An inducible promoter is a promoter that provides for the turning on and off of gene expression in response to an exogenously added agent, or to an environmental or developmental stimulus. For example, expression can be stimulated from an inducible promoter by factors such as alcohol, acetaldehyde, antibiotics (e.g., tetracycline), steroids, metals and other compounds. An environmentally inducible promoter can induce expression of a gene in response to environmental stimuli such as drought, cold, heat, longer exposure to light, or shorter exposure to light. A bacterial promoter such as the P_(tac) promoter can be induced to vary levels of gene expression depending on the level of isothiopropylgalactoside added to the transformed cells. Steroid inducible promoters have also been employed. Dexamethasone-inducible promoters are activated by introduction of dexamethasone to a cell, tissue, cell culture, or tissue culture. The alc promoter system from the filamentous fungi Aspergillus nidulans can be induced by alcohol (e.g., ethanol) or acetaldehyde (see, e.g., Schaarschmidt et al., Plant & Cell Physiol 45(11): 1566-77 (2004). The nopaline synthase (nos) promoter is inducible by hydrogen peroxide and/or methyl jasmonate (see, e.g., Sai & An, Plant Physiol. 109(4): 1191-97 (1995)). Further examples of suitable promoters include lac, tac, trp, phoA, Ipp, Arab, tet and T7.

Nucleotide segment(s) encoding the subunits of the modified microcompartments and, optionally, the additional enzymes or components for providing nanobiocatalytic functions can be combined with a selected promoter by available methods to yield an expression cassette, for example, as described in Sambrook et al. (MOLECULAR CLONING: A LABORATORY MANUAL. Second Edition (Cold Spring Harbor, NY: Cold Spring Harbor Press (1989): MOLECULAR CLONING: A LABORATORY MANUAL. Third Edition (Cold Spring Harbor, NY: Cold Spring Harbor Press (2000)). Briefly, a plasmid containing a promoter such as a T7 promoter can be constructed or obtained (e.g., pET-11 vector). Such plasmids can be constructed to have multiple cloning sites having specificity for different restriction enzymes downstream from the promoter. The nucleotide segment(s) can be subcloned downstream from the promoter using restriction enzymes and positioned to ensure that the nucleotide segment(s) is inserted in proper orientation with respect to the promoter so that the DNA can be expressed. Once the nucleotide segment(s) is operably linked to a promoter, the expression cassette so formed can be subcloned into a plasmid or other vector (e.g., an expression vector).

The expression cassette can also optionally include 3′ nontranslated regulatory DNA sequences that act as a signal to terminate transcription and allow for the polyadenylation of the resultant mRNA. Many 3′ nontranslated regulatory sequences are already present in plasmids available from commercial sources such as Clontech, Palo Alto, Calif. The 3′ nontranslated regulatory sequences can be operably linked to the 3′ terminus of the nucleotide segment(s) by standard methods.

In order to improve identification of host cells that include nucleotide segment(s) encoding the subunits of the modified microcompartments (and, optionally, the additional enzymes or components for providing nanobiocatalytic functions), a selectable or screenable marker gene can be employed. “Marker genes” are genes that impart a distinct phenotype to cells expressing the marker gene and thus allow such transformed cells to be distinguished from cells that do not have the marker. Such genes may encode either a selectable or screenable marker, depending on whether the marker confers a trait which one can ‘select’ for the marker by chemical means, i.e., through the use of a selective agent (e.g., an antibiotic, a visible signal, or the like), or whether marker is simply a trait that one can identify through observation or testing, i.e., by ‘screening.’. Many examples of suitable marker genes are known to the art and can be employed in the practice of the invention.

Included within the terms selectable or screenable marker genes are also genes which encode a “secretable marker” whose secretion can be detected as a means of identifying or selecting for transformed cells. Examples include markers which encode a secretable antigen that can be identified by antibody interaction, or secretable enzymes that can be detected by their catalytic activity. Secretable proteins fall into a number of classes, including small, diffusible proteins detectable, e.g., by ELISA.

An expression cassette can also include plasmid DNA. Plasmid vectors include additional DNA sequences that provide for easy selection, amplification, and transformation of the expression cassette in prokaryotic and eukaryotic cells, e.g., pUC-derived vectors such as pUC8, pUC9, pUC18, pUC19, pUC23, pUC119, and pUC120, pSK-derived vectors, pGEM-derived vectors, pSP-derived vectors, or pBS-derived vectors. The additional DNA sequences include origins of replication to provide for autonomous replication of the vector, additional selectable marker genes (e.g., antibiotic), unique multiple cloning sites providing for multiple sites to insert DNA sequences or genes encoded in the expression cassette and sequences that enhance transformation of prokaryotic and eukaryotic cells.

Expression cassettes and/or vectors that include nucleotide segment(s) encoding the subunits of the modified microcompartments (and, optionally, the additional enzymes or components for providing nanobiocatalytic functions) can be introduced into host cells by a variety of methods. For example, such expression cassettes and/or vectors can be introduced into a recipient cell to create a transformed cell by available procedures. It is likely that not all recipient cells receiving DNA segments or sequences will result in a transformed cell wherein the DNA is stably integrated into the host cell genome and/or expressed.

The host cell can be any type of prokaryotic or eukaryotic cell. In some cases, the host cell is a prokaryotic cell, for example, a bacterial cell. Examples of host cells that can be employed include Haliangium ochraceum or Escherichia coli.

Properties of Bacterial Shell Proteins and/or Microcompartments

As described herein, a BMC shell protein that was naturally devoid of any cofactor was used as a template for structure-based rational design of a [4Fe-4S] cluster-binding site. As illustrated by a combination of structural and spectroscopic techniques, the assembly of the cluster in the engineered protein is efficient and specific; at least 72-74% of the proteins bind a [4Fe-4S] cluster, and no other forms of the cluster were detected. The cluster and the ligating cysteine residues are hydrogen-bonded to the main chain of the protein. These interactions likely contribute to the stability of the [4Fe-4S] cluster, and facilitate its redox reversibility. For example, in some cases even when the encapsulated [4Fe-4S] cluster is exposed to solvent, it is relatively resistant to stresses such as high temperature or high concentrations of urea. Significantly, the encapsulated cluster exhibits redox and spectroscopic characteristics of [4Fe-4S] clusters found in low-potential bacterial ferredoxins. The structural data reveals a binding mode reminiscent of those found in diverse classes of enzymes with only three irons coordinated by cysteine residues.

BMC-T1-S55C provides a means for achieving electron transfer across the shell of BMCs and allows new functionalities to be usefully incorporated into BMCs, including tailor-made encapsulated oxidoreductive pathways.

The data reported herein is the first structural evidence for the successful design of a binding site for a [4Fe-4S] cluster into a protein scaffold, specifically a constituent shell protein of a bacterial organelle. Using a structure-guided approach, the pore of BMC-T1 was re-engineered to selectively incorporate a [4Fe-4S] cluster. Mononuclear Fe, and [2Fe-2S] or [3Fe-4S] clusters were not observed as demonstrated by spectroscopic and structural characterization. The [4Fe-4S] cluster exhibits EPR and redox properties reminiscent of those in low-potential bacterial ferredoxins (FIGS. 4B and 5A).

The BMC-T1-S55C monomer scaffold is composed of two domains which have complementary roles: the first domain harbors the [4Fe-4S] cluster-binding site (Cys55), while residues within the second domain (Gly155 and Ala157) provide hydrogen bonding interactions that most likely stabilizes the [4Fe-4S] cluster and facilitates its redox reversibility. In most [Fe—S] cluster proteins, the cluster ligands are on the same polypeptide chain; in contrast, each BMC-T1-S55C protomer contributes one-third of the [4Fe-4S] cluster binding site, which is completed by the trimerization. Three cysteinate ligands are sufficient for [4Fe-4S] incorporation. The fourth ligand can vary; for example, in radical SAM enzymes, when SAM is present it is the fourth ligand. Similarly to activated aconitase and other dehydratase enzymes, a water molecule (or hydroxide ion) completes the primary coordination sphere of the cluster in BMC-T1-S55C (FIG. 3B). Therefore, the [4Fe-4S] cluster of BMC-T1-S55C can be considered a hybrid between clusters found in low-potential bacterial ferredoxins (redox and spectroscopic characteristics) and those found in different classes of enzymes (architecture of the cluster).

The reduction potential value of −370 mV at pH 7.5 (FIG. 5A) is at the more positive end of the range of −374 to −500 mV reported for bacterial ferredoxins (Rouault, T. Iron-Sulfur Clusters in Chemistry and Biology; De Gruyter: Berlin, 2014) but is well within the range of −700 to +100 mV reported for [4Fe-4S]^(2+/+) clusters for other [Fe—S] cluster proteins (Johnson, M. K.; Smith, A. D. In Encyclopedia of Inorganic and Bioinorganic Chemistry; John Wiley & Sons, Ltd: Online, 2011). In comparison to other designed [4Fe-4S] proteins, the reduction potential of BMC-T1-S55C is comparable to the value of −350 mV (at pH 8) reported for the minimal ferredoxin maquette (Gibney et al Proc. Natl. Acad. Sci. U.S.A. 93: 15041 (1996)) but is significantly more positive than the value reported for the DSD-Fdm (Domain-Swapped Dimer-Ferredoxin maquette) of −479 mV (at pH 7.5) (Roy et al. Am. Chem. Soc. 136: 17343 (2014)), as well as the minimal photosystem I F_(A)- and F_(B)-maquettes of −440 mV and −470 mV (at pH 8.3), respectively (Antonkine et al. Biochim. Biophys. Acta 1787: 995 (2009). The similarity of the reduction potential between BMC-T1-S55C and the minimalist ferredoxin maquette may reflect the degree of solvent exposure of the clusters in both systems, whereas the more negative potential of DSM-Fdm may be due, at least in part, to the burial of the cluster in the hydrophobic core of its three-helix bundle scaffold.

Notably, the reduction potential of BMC-T1-S55C is much lower than the value determined for the [4Fe-4S] cluster of PduT from C. freundii, +99 mV (at pH 7) (Parsons et al. J. Biol. Chem. 283: 14366 (2008)). This demonstrates that BMC shell proteins can incorporate [4Fe-4S] clusters with a wide range of reduction potentials, indicating that modifying the environment of the cluster will allow the fine-tuning of the reduction potential of the BMC-T1-S55C [4Fe-4S] cluster to the requirements of the BMC-encapsulated enzymes.

The capacity of the BMC-T1-S55C cluster to function as an electron relay is illustrated by its ability to cycle between oxidized and reduced states without being degraded or oxidatively damaged (FIG. 5B). This is in contrast to other designed [4Fe-4S] cluster proteins in which the reduced state is unstable and irreversible (Grzyb et al. Biochim. Biophys. Acta 1797: 406 (2010)).

Hydrogen bonding plays a role in folding and stability of proteins, and influences the properties of metal centers. The installation of a hydrogen bond network is an important consideration in metalloprotein design. The presence of second shell hydrogen bond interactions between backbone amides (Gly155) and the thiolate ligands of Cys55 (FIG. 3B) likely confers stability to the BMC-T1-S55C [4Fe-4S] cluster upon redox cycles. The presence of the hydrogen bond network in the BMC-T1 scaffold which stabilizes the metal center is an important component of the design. The robustness of the cluster is also illustrated by its resistance to different stressors. For example, BMC-T1-S55C retains a significant amount of intact bound [4Fe-4S] cluster after incubation at 55° C., is used as a first purification step. Characterization of the stability of the trimer with and without the cluster, shows that the holoprotein is more stable in urea than the apoprotein (FIG. 6A-6D).

The BMC-T1-S55C cluster seems somewhat tolerant to oxygen. Indeed, initial purifications of BMC-T1-S55C were performed under aerobic conditions from aerobically grown cultures. The purified protein retained a brown color for a few weeks at 4° C., without bleaching of the chromophore or any precipitation. Another indication of oxygen tolerance is the presence of the intact cluster in the BMC-T1-S55C structure, even though preparing the crystals for data collection required brief exposure to aerobic conditions. However, a combination of UV-Vis and EPR spectroscopies suggests that the degradation of the cluster to a [3Fe-4S] form may start shortly after oxygen exposure and can continue over time. The [3Fe-4S] is in turn converted to a more stable [2Fe-2S] form (FIG. 6E-6F). In the crystals, during the brief subjection to aerobic conditions prior to data collection, surface proteins likely may come into contact with oxygen. However, clusters deeper in the crystal are relatively shielded by other proteins as well as the solvent environment, and so their metal centers are less prone to degradation.

To date, there is only a single report of the successful incorporation of a [4Fe-4S] cluster into a natural protein normally devoid of any cofactors, but the electrochemistry of that cluster demonstrates that it is a high potential iron-sulfur protein accessing the [4Fe-4S]^(3+/2+) couple (Coldren et al. Proc. Natl. Acad. Sci. U.S.A. 94: 6635 (1997). Moreover, there has been no structural evidence for the success of any of the [4Fe-4S] protein designs described above. The ability to transfer electrons into and out of BMC shells opens a new frontier in their applications in synthetic biology.

In addition to BMC-T1-S55C, additional mutants have been generated to fine-tune the reduction potential of the engineered [4Fe-4S] cluster. BMC-T1-S56C possesses a binding site that is distinct from the one in BMC-T1-S55C, with a different orientation and environment: the reduction potential is decreased to −455 mV vs. SHE (FIG. 11A). In BMC-T1-S55C/S56C, the C55 binding site is occupied by a [4Fe-4S] cluster, as shown by its crystal structure. UV-Vis and EPR spectroscopies (FIG. 8). The presence of additional cysteine residues (C56) increases the reduction potential to −310 mV vs. SHE (FIG. 11A). Like BMC-T1-S55C, these clusters have also been shown to be redox active and stable through redox cycles, providing a cofactor capable of sustaining efficient electron transfer. Moreover, these different mutant building blocks retain the ability to be incorporated into synthetic shells, as shown by SDS-PAGE analysis of purified shells (FIG. 9). This demonstrates that engineering BMC-T1 does not disrupt the formation of the shells, opening the way to use these different variants to transfer electrons across the shell of bacterial microcompartments or for potential incorporation in 2-dimensional scaffolds.

The addition in these three variants of an I154F mutation modifies the UV-Vis and EPR signatures of the clusters (FIG. 10), demonstrating a modification of their environment and of their reduction potential. For example, a reduction potential of about −460 mV vs. SHE (FIG. 11B) was estimated during the preliminary characterization of the [4Fe-4S] cluster present in BMC-T1-S55C/I154F. This library of engineered shell proteins provides optimal subunit pairings for the encapsulated pathway and the electron transfer module.

The following non-limiting Examples illustrate how aspects of the invention have been developed and can be made and used.

Example 1: Materials and Methods

This Example describes some of the materials and methods used in developing the invention.

Plasmids, Bacterial Strains and Growth Conditions

A nucleic acid segment encoding BMC-T1 was subcloned in a pET 11 plasmid DNA vector from a previously described DNA construct (Lassila et al. 2014 JMB) coding for the seven shell proteins of the synthetic shells.

The BMC-T1 has the following amino acid sequence (SEQ ID NO: 1).

  1 MDHAPERFDA TPPAGEPDRP  ALGVLELTSI ARGITVADAA  41 LKRAPSLLLM

  LMMRGQVAEV EESMIAAREI  81 AGAGSGALLD ELELPYAHEQ  LWRFLDAPVV ADAWEEDTES 121 VIIVETATVC AAIDSADAAL  KTAPVVLRDM RLAIGIAGKA 141 FFTLTGELAD VEAAAEVVRE  RCGARLLELA CIARPVDELR 181 GRLFF

A modification of the BMC-T1 structure involving substitution of serine at position 55 with a cysteine (S55C) was made in the BMC-T1 gene using the QuikChange Lightning site-directed mutagenesis kit (Agilent Technologies) using the instructions provided by the manufacturer. An amino acid sequence for the S55C-modified BMC-T1 protein is as follows (SEQ ID NO:3).

  1 MDHAPERFDA TPPAGEPDRP  ALGVLELTSI ARGITVADAA  41 LKRAPSLLLM

LMMRGQVAEV EESMIAAREI  81 AGAGSGALLD ELELPYAHEQ LWRFLDAPVV ADAWEEDTES 121 VIIVETATVC AAIDSADAAL  KTAPVVLRDM RLAIGIAGKA 141 FFTLTGELAD VEAAAEVVRE  RCGARLLELA CIARPVDELR 181 GRLFF

The plasmids containing the sequence coding for BMC-T1 (pCA14) and BMC-T1-S55C (pCA15) were transformed in E. coli BL21 (DE3) for heterologous expression.

For the aerobic production of BMC-TL, the corresponding recombinant E. coli strain was grown in LB broth Miller with 100 μg/liter ampicillin at 37° C., with agitation (160 rpm) to an optical density at 600 nm of 0.6, then induced with 0.45 μM isopropyl thio-β-D-thiogalactoside (IPTG) and grown for another 15 hours at 22° C. The cells were then harvested and stored at −80° C.

The anaerobic production of BMC-T1-S55C was performed by a modified protocol from Kuchenreuther et al. (PLoS One 5(11): e15491 (2010)). Cultures were grown in a MOPS/NaOH buffered (100 mM, pH 7.5) LB-medium. First, bottles containing MOPS buffer were sparged with nitrogen gas to remove oxygen. The bottles were capped (using rubber caps) and transferred into an anaerobic chamber (Coy, Grass Lake, Mich.). The buffer was then supplemented with LB broth MILLER granulates (EMD Millipore). The bottles were sealed with rubber stoppers and autoclaved. The sterile media bottles were then anaerobically supplemented with 25 mM glucose, 25 mM sodium fumarate, 1 mM L-cysteine, 1 mM ferric ammonium citrate, 100 μg/liter ampicillin. The bottles were then inoculated (2% v/v) with an aerobically grown pre-culture. The anaerobic cultures were grown at 37° C., with agitation (120 rpm). When the cultures reached an optical density at 600 nm of 1, the culture was induced with 1 mM IPTG and grown for another 20 h at the same temperature. The cells were harvested and stored at −80° C., under anaerobic conditions.

Protein Purification and [Fe—S] Cluster Reconstitution.

BMC-T1 was purified as follows: cells (typically from 1 L E. coli culture) were resuspended in 50 mM Tris/HCl pH 7.5.75 mM NaCl (buffer A) (cell wet weight to buffer volume ratio 1:2) in the presence of DNAse and lysed by two consecutive passages through a French Press at a pressure of 137 MPa. This crude lysate was then heated to 55° C., for 30 min to precipitate other proteins (BMC-T is relatively stable at this temperature). This step was followed by centrifugation at 8,000 g for 20 min to pellet the precipitated proteins and cell debris. The supernatant was filtered through a 0.22 μm filter and loaded on a Tosoh Toyopearl SuperQ column equilibrated in buffer A. The protein was eluted using a gradient from 75 mM to 500 mM NaCl in 10 column volumes. Fractions showing the presence of the protein on SDS-PAGE were pooled and concentrated using an Amicon centrifugal concentrator (30 kDa cut-off). The protein was then applied to a gel filtration column (HiLoad 16/600 Superdex 75 pg. GE Healthcare) equilibrated with a 50 mM Tris/HCl pH 7.5, 150 mM NaCl buffer. The purified proteins were then stored at 4° C. Purified BMC-T1 was buffer-exchanged to 10 mM Tris/HCl pH 7.5 using a PD-10 column (GE Healthcare), and concentrated to 5.5 mg/ml for crystallization.

BMC-T1-S55C was purified as described above in an anaerobic chamber (Coy, Grass Lake, Mich.), typically from a 6 L anaerobic E. coli culture and using a MOPS/NaOH buffer system instead of Tris/HCl. Buffers used for the purification were degassed and allowed to equilibrate with the anaerobic chamber atmosphere (95% N₂, 5% H₂) for at least one day prior to use. After anion exchange chromatography, the sample was subjected to [Fe—S] cluster reconstitution under anaerobic conditions: the diluted protein was incubated with 10 mM DTT for 1 hour at 4° C., then FeCl₃ was added to a final concentration of 400 μM and followed by a 3-4 h incubation at 4° C. Finally, the same concentration of Na₂S was added, and the sample was incubated at 4° C., overnight, before being concentrated, filtered and purified using gel filtration. For crystallization experiments, reconstituted BMC-T1-S55C was buffer exchanged to 10 mM MOPS/NaOH pH 7.5, 10 mM NaCl, 10 mM DTT and concentrated to 8.5 mg/ml.

Protein concentrations were determined using the bicinchoninic acid (BCA) kit (Sigma-Aldrich). Iron content was determined by the ferrozine method (Stookey, L. L. Anal. Chem. 1970, 42, 779).

Crystallization and Structure Determination

BMC-T1 crystals were obtained by mixing 2 μl of protein with an equal volume of a reservoir condition containing 30 mM citric acid, 70 mM BIS-Tris propane (final pH 7.6) and 18% PEG 3.350. Crystals were cryoprotected using PEG 400 at a final concentration of 25%. BMC-T1-S55C crystals were grown in sitting drops using 250 mM sodium acetate, 100 mM Tris/HCl pH 8.5, 26% PEG 4,000 as reservoir condition (protein/reservoir ratio of 1:1). Cryoprotection was achieved using 38% 1,2-propanediol and 21% 2-methyl-2,4-pentanediol (MPD; final concentrations). Stabilized crystals were flash frozen in liquid nitrogen until data collection. For BMC-T1-S55C, all steps (except looping and freezing steps) were conducted in a Coy anaerobic chamber (Coy, Grass Lake, Mich.). X-ray diffraction data were collected at beamline 12-2 of the Stanford Synchrotron Radiation Lightsource (BMC-T1) and at the Advanced Light Source at Lawrence Berkeley National Laboratory beamline 5.0.3 (BMC-T1-S55C, 100 K, 1,0000 Å wavelength). Diffraction data were integrated with XDS (Kabsch, Acta Crystallogr. D Biol. Crystallogr. 66: 125 (2010)) and scaled with SCALA (CCP4, Winn et al. Acta Crystallogr. D Biol. Crystallogr. 67: 235 (2011)). The BMC-T1 structure was solved by molecular replacement (MR) in Phaser (McCoy, J Appl Crystallogr 40: 658 (2007)) using a carboxysome BMC-T protein, CsoS1D from Prochlorococcus marinus (PDB ID: 3FCH) as the search model. Autobuilding was performed using phenix.autobuild (Adams et al. Acta Crystallogr. D Biol. Crystallogr 66: 213 (2010)) followed by cycles of manual rebuilding in COOT²⁸ (Emsley & Cowtan, Acta Crystallogr. D Biol. Crystallogr 60: 2126 (2004)) and refinement with phenix.refine (Adams 2010), which also performed the automatic water picking. The structure of BMC-T 1-S55C was solved using molecular replacement with the structure of BMC-T1. Statistics for diffraction data collection, structure determination and refinement are summarized in Table 1.

TABLE 1 Data collection and refinement statistics BMC-T1 BMC-T1-S55C Data collection Space group P 2₁ P 1 Cell dimensions a, b, c (Å) 69.63 66.38 122.25 42.9 55.6 117.9 α, β, γ (°) 90.0 92.4 90.0 83.5 81.2 87.0 Resolution (Å) 31.51-2.44 (2.58-2.44)* 38.62-1.80 (1.87-1.80)* R_(merge) 0.107 (0.417) 0.054 (0.610) I/σI 8.3 (3.1) 11.3 (1.4)  Completeness (%) 96.5 (93.3) 96.6 (91.3) Redundancy 3.3 (3.3) 2.1 (2.0) Refinement Resolution (Å) 31.5-2.44 38.6-1.80 No. reflections 74,297 176,094 R_(work/)R_(free) 23.3/27.7 18.1/22.3 No. atoms 9,018 9,244 Protein 8,687 8,821 Ligand/ion — 16 Water 331 407 B-factors 39.0 33.4 Protein 39.4 33.1 Ligand/ion — 28.2 Water 40.1 39.8 R.m.s deviations Bond lengths (Å) 0.003 0.019 Bond angles (°) 0.597 1.96 1 crystal per dataset, *Values in parentheses are for highest-resolution shell.

The final model had 93.8% and 95.9% of the residues in the favored, 6.1% and 3.9% in the allowed and 0.1% and 0.2% in the disallowed region of the Ramachandran plot for BMC-T1 and BMC-T1-S55C, respectively. Figures of structural models were prepared using PyMOL (www.pymol.org). Atomic coordinates and structure factors (PDB ID: 5DIH for BMC-T1 and 5DII for BMC-T1-S55C) have been deposited in the Protein Data Bank (see website at pdb.org).

Optical Spectroscopy.

UV-vis spectra were recorded in anaerobic conditions using an Agilent Technologies Cary60 UV-Vis spectrophotometer. For reduction tests, proteins (in 50 mM MOPS/NaOH pH 7.5, 75 mM NaCl) were mixed in anaerobic conditions with 0.5 mM sodium dithionite and incubated for 5-10 min before recording the spectra.

Electron Paramagnetic Resonance (EPR).

Continuous wave EPR experiments at variable temperatures (5-70 K) were carried out at a Bruker ESP300 spectrometer equipped with a continuous flow cryostat (Oxford Instruments) and a Bruker ER/4102 ST rectangular resonator which operates in the TE₁₀₂ (9.48 GHz) perpendicular mode. The microwave frequency was measured with a 5350B Hewlett Packard frequency counter. For all experiments, custom-made quartz tubes of the same inner and outer diameter were used (QSI). Quantitation of the signals was carried out by measuring a 256 μM Cu²⁺-EDTA standard under non-saturating conditions by double numerical integration of the first-derivative experimental and simulated EPR spectra. All quantifications were carried out for the spectra recorded at T=10 K. The first-derivative EPR spectra were simulated using the MATLAB (Mathworks) based Easyspin simulation software (Stoll & Schweiger, A. J. Magn. Reson. 178: 42 (2006). The samples were transferred to the EPR tubes under anaerobic conditions and were quickly frozen in liquid nitrogen in a Coy anaerobic chamber prior to measuring.

Redox Potentiometry.

Chemical redox titrations were performed as described by Dutton (Methods Enzymol. 54: 411 (0.1978)) and all values are reported relative to the SHE. Titrations were performed in aqueous solutions containing 60 μM iron-sulfur cluster protein in 50 mM MOPS/NaOH pH 7.5, 75 mM NaCl with the following mediators: anthraquinone-2,6-disulphonate (0.6 μM), anthraquinone-2-sulphonate (0.6 μM), benzyl viologen (0.2 μM) and methyl viologen (0.2 μM). Reduction was accomplished with sodium dithionite and re-oxidation with duroquinone. The normalized absorbance change at 422 nm (selected to eliminate the contribution of the viologen dyes) due to [4Fe-4S] cluster reduction was fitted to an N=1 Nernst equation.

Example 2: Structural Characterization of BMC-T1

Synthetic HO shells were derived from a BMC of unknown function encoded in the genome of the mycobacterium Haliangium ochraceum (see, e.g., Lassila et al., J. Mol. Biol. 426: 2217 (2014); Axen et al., PLoS Comput. Biol. 10: e1003898 (2014)). The synthetic HO shells were composed of seven gene products: four BMC-T1-T3 and one BMC-H protein (FIG. 1; Lassila et al., J. Mol. Biol. 426: 2217 (2014)).

BMC-T1 (locus tag: Hoch_5812) was selected for characterization and as a scaffold for the incorporation of a metal center because it forms trimers that incorporate into single layered facets of the synthetic shell.

Haliangium ochraceum shell proteins tend to be only distantly related to their counterparts in experimentally characterized BMCs (e.g. the propanediol utilization and ethanolamine utilization BMCs and the carboxysome). For example, a BLAST search of the non-redundant sequence database indicates the closest homolog of BMC-T1 is a BMC-T protein encoded in the genome of Hyalangium minutum (which also belongs to the Myxococcales) with 49% identity. The next closest homologs share only 37% identity or less with BMC-T1. In a query of the Protein Data Bank (PDB), three hits, each 36% identical at the level of primary structure, were returned: PduT, a BMC-T protein of the propanediol utilization BMC of Salmonella enterica (PDB ID 3N79) and Citrobacter freundii (PDB ID 3PAC), as well as a homolog from a glycyl radical enzyme-associated BMC³ identified in Desulfitobacterium hafniense (PDB ID 3NWG). Given this relatively remote sequence homology to structurally characterized BMC shell proteins, the structure of BMC-T1 Wild Type (WT) was determined to guide the design of a [4Fe-4S] cluster-binding site.

The BMC-T1 wild type protein was over-expressed in Escherichia coli, and the purified protein was crystallized in the monoclinic space group P 2₁. The crystals diffracted to a resolution of 2.4 Å (Table 1), and the structure was solved by molecular replacement using CsoS1D from Prochlorococcus marinus (PDB ID: 3FCH) as the search model. There were six subunits (two trimers) per asymmetric unit; the trimer structure is shown FIG. 2A. Due to disordered termini and loops, varying numbers of amino acids (between 3 and 23 residues per chain) had to be omitted from the N-termini and some loop regions of the three monomers. Data collection and refinement statistics are provided in Table 1.

Example 3: Structure-Based Rational Design of a [4Fe-4S] Cluster Binding Site into BMC-T1

The structure of BMC-T1 was used to design a [4Fe-4S] cluster-binding site at the cyclic axis of symmetry of the trimer. The hydroxyl side chains of Ser55 from each protomer are arranged in a trigonal plane with O_(γ)-O_(γ) distances between 6.46 and 6.74 Å (FIGS. 2B and 2D). This arrangement is reminiscent of the S_(γ)-S_(γ) bite distances of cysteine residues coordinating [4Fe-4S] clusters in natural ferredoxins (Petros et al., Inorg. Chem. 45: 9941 (2006)). The inventors hypothesized that the pore formed at the symmetry of the BMC-T1 trimer could serve as a [4Fe-4S] cluster-binding site. The side chains of the three Ser55 residues (one from each protomer) point towards the concave side of the trimer (FIG. 2A, 2C) and are in a gauche(+) conformation with χ₁ angles of 111-112° (FIG. 2B-2C). Furthermore, the rigid β-turn motif that contains Ser55 disfavors structural rearrangement to accommodate a rubredoxin-type mononuclear iron that requires a smaller bite distance of 3.8 Å (Petros 2006). In view of the geometry and bite distance, and the three-fold symmetry axis (pore), the inventors decided to substitute Ser55 with a cysteine to accommodate binding of a [4Fe-4S] cluster (referred to as BMC-T1-S55C).

Example 4: The Structure of BMC-T1-S55C Confirms Incorporation of a [4Fe-4S] Cluster

Because [4Fe-4S] clusters are typically oxygen-sensitive, purification of BMC-T1-S55C was conducted in anaerobic conditions using the same purification protocol as described for the wild type protein. In stark contrast to the colorless wild protein, purified BMC-T1-S55C exhibited a brown color, indicating the presence of an [Fe—S] cluster (FIG. 2E). Size exclusion chromatography confirmed that BMC-T1-S55C is a trimer (FIG. 2F-2G).

BMC-T1-S55C was crystallized anaerobically, and the structure was solved at 1.8 Å resolution by molecular replacement using the wild type structure as the search model (Table 1). There are two trimers in the asymmetric unit of the P1 space group. The electron density was of high quality, with only a few (<6) residues at the N-termini and in some flexible loops (Ala14, Gly15, and Glu116-Thr118) that could not be modeled due to disorder. Both trimers contain electron density that could be readily modeled as a [4Fe-4S] cluster in the middle of the central, positively charged pore (FIG. 3A-3D). The electron density is well-defined, and the positions of the iron atoms were confirmed by their anomalous signal (FIG. 3E-3F). The occupancy for the [4Fe-4S] cluster was refined to 72-74%.

Using the ferrozine assay to measure metal content, about 60% of the protein was estimated to contain a [4Fe-4S] cluster, consistent with the results of the structure determination. Three of the iron atoms of each cluster are coordinated by the three introduced cysteines (S55C), and a water or hydroxide molecule ligates the fourth unique iron (FIG. 3B). The S_(γ) Cys55-Fe and Fe—OH₂/OH bonds have distances of 2.3 Å and 2.1 Å, respectively. The Fe—S bonds within the cluster have an average length of 2.2 Å. The Fe—Fe distance is 2.8 Å. These values are comparable to those observed in a variety of [4Fe-4S] cluster proteins and synthetic [4Fe-4S] cluster analogs (Fe—S distances of ˜2.3 Å and Fe—Fe distances of ˜2.5-2.8 Å) (Stout, in Encyclopedia of Inorganic and Bioinorganic Chemistry; John Wiley & Sons. Ltd: Online (2011); Giastas et al., J. Biol. Inorg. Chem. 11: 445 (2006); Mitra et al., J. Am. Chem. Soc. 135: 2530 (2013); Herskovitz et al., Proc. Natl. Acad. Sci. U.S.A. 69: 2437 (1972)). Moreover, three of the cluster sulfides make hydrogen bonds with the amide backbone of residues Ala157 (of each protomer) with H to S distances of 2.7-2.8 Å (N to S distances of 3.4-3.5 Å) (FIG. 3B); these are comparable to main chain-cluster bonds observed in other [4Fe-4S] cluster-containing proteins (Giastas 2006; Fukuyama, In Encyclopedia of Inorganic and Bioinorganic Chemistry; John Wiley & Sons, Ltd: Online (2011)). The sulfur atoms of Cys55 are hydrogen-bonded to the backbone amide of Gly155 with S to H distances of 2.1-2.2 Å (S to N distances of 3.1-3.2 Å) (FIG. 3B). These hydrogen bonds are also present in the BMC-T1 (wild type) structure (amide backbone of Gly155 and O_(γ) of the Ser55 side chain), demonstrating that the Ser55 to Cys55 mutation did not perturb the overall structure of BMC-T1. This is further corroborated by a structural superposition of BMC-T1 and BMC-T1-S55C (FIG. 3G); the RMSD (root-mean-square deviation) for 160 α-carbon atom pairs is 0.5 Å. Furthermore, the conformation of the three cysteine residues is conserved with respect to their serine equivalent (χ₁ angle of ˜110°). Overall, the structure validates the original design criteria, and most importantly, it represents the first structure of a designed [4Fe-4S] protein.

Example 4: Characterization of the [4Fe-4S] Cluster in BMC-T1-S55C by Optical Spectroscopy

The UV-Visible (UV-Vis) spectrum of BMC-T1 does not show any absorbance features other than the 280 nm band of the aromatic residues (FIG. 4A). In contrast, after [Fe—S] cluster reconstitution of BMC-T1-S55C, the optical spectrum recorded under anaerobic conditions exhibited a broad absorption band at approximately 385 nm (FIG. 4A), which is characteristic of S-to-Fe(III) charge transfer transitions observed in [Fe—S] cluster-containing proteins (Sweeney & Rabinowitz. Annu. Rev. Biochem. 49: 139 (1980); Lippard & Berg. In Principles of Bioinorganic Chemistry; University Science Books: Mill Valley, Calif. (1994)).

In addition, there is no evidence for bands that are typically observed for [2Fe-2S] clusters (features at 310-330 nm, 420 nm, and 465 nm), indicating that the trimer contains exclusively a [4Fe-4S] cluster, as observed in the crystal structure. Treatment with dithionite (−660 mV vs. SHE at pH 7; Mayhew. Eur J. Biochem 85: 535 (1978)) resulted in complete disappearance of the optical features (FIG. 4A), consistent with reduction of the cluster. Based on the [4Fe-4S] cluster occupancy in the crystal structure, the extinction coefficient at 385 nm is between 18,000-19,000 M⁻¹·cm⁻¹, which is within the range reported for other [4Fe-4S] clusters (16,000-23,000 M⁻¹·cm⁻¹; Sweeney & Rabinowitz 1980). Furthermore, similar results were obtained with the non-reconstituted BMC-T1-S55C, although the [4Fe-4S] cluster band was less intense (FIG. 4C). This indicates a lower efficiency in cluster incorporation; we estimated that about 50% of the protein spontaneously binds a cluster in vivo. Enhancement in cluster incorporation by chemical reconstitution is well known, especially in the case of O₂-sensitive [Fe—S] cofactors or when overexpressing the [Fe—S] containing proteins in the absence of the auxiliary Iron-Sulfur Cluster maturation machinery (Lanz et al., Methods Enzymol. 516: 125 (2012)).

Example 5: Characterization of the [4Fe-4S] Cluster in BMC-T1-S55C by EPR Spectroscopy

The continuous wave (CW) X-Band EPR spectrum of BMC-T1 (with and without dithionite) exhibited no paramagnetic signals attributable to [Fe—S] clusters (FIG. 4B), which is in agreement with its UV-Vis spectrum. In contrast, after reduction with dithionite, both the purified, non-reconstituted and the chemically reconstituted BMC-T1-S55C proteins exhibited qualitatively comparable EPR spectra that are reminiscent of [4Fe-4S] clusters (FIG. 4B, 4D-4E). The degree of [4Fe-4S] cluster incorporation in BMC-T1-S55C was consistently higher in the chemically reconstituted protein than in the non-reconstituted form, which again corroborates the results of the UV-Vis analysis. The EPR spectrum of the reconstituted, chemically reduced BMC-T1-S55C was characterized by an axial signal with g_(av) of 1.98 and principal g-values 2.04 and 1.91, respectively. The intensity of this signal was strongly temperature-dependent and was barely detectable at temperatures above 45 K (FIG. 4B). The effective g-values and the relaxation properties were typical of those reported for [4Fe-4S]⁺¹ clusters with an S value of ½ ground state.⁴¹ In the case of the non-reconstituted BMC-T1-S55C sample reduced with dithionite, the EPR signal, albeit very similar, exhibited a slight downshift in the low-field g-component, small changes in the rest g-values, and broader linewidths (FIG. 4E). These observations indicate a higher degree of heterogeneity with respect to the reconstituted sample, which can be attributed to the formation of clusters in slightly different local protein environments. The EPR signals of the assembled [4Fe-4S] cluster in BMC-T1-S55C varied only marginally between different protein preparations; changes in small g-values shifts and overall signal line shape broadness, indicating that the incorporated cluster is rather sensitive to local changes in its protein environment (FIG. 4D). In some cases, an additional low-field signal at g˜2.11 was detected, indicating the presence of a second cluster form. After reconstitution, the intensity of this component was markedly reduced, consistent with a conclusion that the [4Fe-4S] cluster incorporated in the chemically reconstituted samples exhibits less heterogeneity (FIG. 4D). The g˜2.11 signal may be associated with a different orientation of the [4Fe-4S] cluster, in which the water/hydroxide-ligated iron would be oriented towards the concave face of the trimer instead of being located in the pore, or to a different coordination state where the water molecule may be replaced by an inorganic or protein ligand.

To determine if any [3Fe-4S] clusters were present in BMC-T1-S55C, the EPR spectra were measured prior to reduction with dithionite (in both its non-reconstituted and reconstituted forms). No signals attributable to [3Fe-4S]¹⁺ clusters were detected (g_(av) about 2.01) (FIG. 4E), thus confirming that only [4Fe-4S] clusters were assembled. In addition, in the reconstituted sample without dithionite, a small amount (about 20% of the total cluster content) of [4Fe-4S]¹⁺ clusters could be observed, indicating that under these conditions an appreciable fraction of the clusters was partially reduced. Overall, the assembled [4Fe-4S] cluster in BMC-T1-S55C exhibited EPR signals and relaxation properties highly reminiscent of those observed in classical [4Fe-4S]¹⁺ low-potential ferredoxins.

Example 6: Spectroelectrochemistry of BMC-T1-S55C

The midpoint reduction potential, E_(m), of BMC-T1-S55C was determined using UV-Vis detected spectroelectrochemistry (FIG. 5A). The reduction potential of the [4Fe-4S] cluster in BMC-T1-S55C was determined to be −370 mV vs. SHE (±10 mV), which is in agreement with the efficient reduction of the cluster by dithionite. This value also explains the observation of partially reduced clusters after incubation with DTT (−332 mV at pH 7) (Cleland, Biochemistry 3: 480 (1964)) during the chemical reconstitution of the cluster (FIG. 4E). Furthermore, reduction of the cluster by dithionite was fully reversible upon addition of duroquinone as an oxidant. Successive reduction/oxidation cycles were repeated without any degradation of the [4Fe-4S]²⁺ cluster UV-Vis signature at ˜385 nm (FIG. 5B).

Example 7: Stability of the [4Fe-4S] Cluster in BMC-T1-S55C Upon Chemical Denaturation and Oxygen Exposure

To test whether the presence of a cluster can stabilize host proteins in the system described herein, a chemical denaturation was performed on BMC-T1 and BMC-T1-S55C using urea with monitoring by circular dichroism (CD) spectroscopy.

The results illustrated in FIG. 6A-6D show that BMC-T1 is fully denatured at 6 M urea. In contrast, BMC-T1-S55C is extremely resistant to chemical denaturation. Very little unfolding was detected even at concentrations of urea as high as 10.2 M (FIG. 6A-6D). Moreover, the UV-Vis spectrum of BMC-T1-S55C in 10.2 M urea exhibits the typical signal at 385 nm (FIG. 6A-6D). These data indicate that BMC-T1-S55C and its [4Fe-4S] cluster are an extremely stable assembly.

The response of the [4Fe-4S] cluster in BMC-T1-S55C toward oxygen was also determined. A sample of the anaerobic protein was exposed to air, and UV-Vis and EPR spectra (without dithionite) were recorded at different time points (FIG. 6E-6F). EPR spectra showed that upon exposure to air, a transient [3Fe-4S]¹⁺ cluster is generated, but to only sub-stoichiometric amounts such as 5 μM. In combination with the observations from UV-Vis spectroscopy, in which a decrease of the [4Fe-4S] charge transfer band is relatively fast and accompanied by features that are somewhat reminiscent of [2Fe-2S] clusters, these results demonstrate that the [4Fe-4S] cluster is indeed susceptible to oxidation by dioxygen. This O₂-dependent degradation appears to proceed via a [3Fe-4S]¹⁺ intermediate (by release of one of the Fe) and later formation of an O₂-unstable [2Fe-2S] cluster to its complete degradation after prolonged exposure (several hours to a day).

None-the-less, the BMC-T1-S55C iron cluster seems somewhat tolerant to oxygen. For example, initial purifications of BMC-T1-S55C were performed under aerobic conditions from aerobically grown cultures. The purified protein retained a brown color for a few weeks at 4° C., without bleaching of the chromophore or any precipitation. Another indication of oxygen tolerance is the presence of the intact cluster in the BMC-T1-S55C structure, even though preparing the crystals for data collection required brief exposure to aerobic conditions.

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All patents and publications referenced or mentioned herein are indicative of the levels of skill of those skilled in the art to which the invention pertains, and each such referenced patent or publication is hereby specifically incorporated by reference to the same extent as if it had been incorporated by reference in its entirety individually or set forth herein in its entirety. Applicants reserve the right to physically incorporate into this specification any and all materials and information from any such cited patents or publications.

The following statements of the invention are intended to describe and summarize various embodiments of the invention according to the foregoing description in the specification.

Statements:

-   -   1. A modified polypeptide comprising at least 95% sequence         identity to SEQ ID NO: 1, 36, or 37 and with at least one amino         acid substitution.     -   2. The modified polypeptide of statement 1, wherein the at least         one amino acid substitution replaces an amino acid in the         modified polypeptide with a cysteine.     -   3. The modified polypeptide of statement 1 or 2, wherein the at         least one amino acid substitution replaces a serine, threonine,         valine, leucine, isoleucine, methionine, aspartic acid,         asparagine, alanine, arginine, aspartic acid, glutamic acid,         glutamine, glycine, histidine, isoleucine, leucine, lysine,         methionine, phenylalanine, proline, or tyrosine amino acid.     -   4. The modified polypeptide of statement 1, 2, or 3, wherein the         at least one amino acid substitution replaces a serine,         threonine, or proline with a cysteine; and/or wherein the at         least one amino acid substitution replaces an isoleucine,         arginine, or alanine with a phenylalanine.     -   5. The modified polypeptide of statement 1-3 or 4, wherein the         at least one amino acid substitution replaces an amino acid         (e.g. a serine, threonine, or proline) with a cysteine at an         amino acid position corresponding to position 55 or 56 of the         SEQ ID NO: 1 sequence; and/or wherein the at least one amino         acid substitution replaces an amino acid (e.g. an isoleucine,         arginine, or alanine) with a phenylalanine at an amino acid         position corresponding to position 154 of the SEQ ID NO: 1         sequence.     -   6. The modified polypeptide of statement 1-4 or 5, wherein the         modified polypeptide comprises at least 96%, or at least 97%, or         at least 98%, or at least 99% sequence identity to SEQ ID NO: 1,         36, or 37.     -   7. The modified polypeptide of statement 1-5 or 6, wherein the         modified polypeptide has at least 97% sequence identity to SEQ         ID NO:3-8, 36 or 37.     -   8. The modified polypeptide of statement 1-6 or 7, which is a         modified tandem BMC-T subunit.     -   9. The modified polypeptide of statement 1-7 or 8, which         assembles into a microcompartment.     -   10. The modified polypeptide of statement 1-8 or 9, wherein the         at least one amino acid substitution replaces an amino acid that         has a side chain that extends into an interior of a         microcompartment in which the modified polypeptide resides.     -   11. The modified polypeptide of statement 1-9 or 10, wherein the         at least one amino acid substitution replaces an amino acid that         has a side chain that extends into a pore of a microcompartment         in which the modified polypeptide resides.     -   12. The modified polypeptide of statement 1-10 or 11, wherein         the modified polypeptide assembles into a trimer.     -   13. The modified polypeptide of statement 1-11 or 12, wherein         the modified polypeptide assembles into a microcompartment that         is about 30-300 nm, or about 40-200 nm in diameter.     -   14. The modified polypeptide of statement 1-12 or 13, wherein         the modified polypeptide assembles into a microcompartment         within a host cell.     -   15. The modified polypeptide of statement 1-13 or 14, wherein         the modified polypeptide assembles into a microcompartment         within a prokaryotic host cell.     -   16. The modified polypeptide of statement 1-14 or 15, wherein         the modified polypeptide assembles into a microcompartment         within a bacterial host cell.     -   17. The modified polypeptide of statement 1-15 or 16, wherein         the modified polypeptide assembles into a microcompartment         within a Haliangium ochraceum or Escherichia coli host cell.     -   18. An expression cassette or expression vector comprising a         promoter operably linked to a nucleotide segment that encodes         the modified polypeptide of statement 1-16 or 17.     -   19. The expression cassette or expression vector of statement         18, wherein the nucleotide segment encoding the modified         polypeptide has a sequence with at least 95% sequence identity         to SEQ ID NO:2 and with at least one nucleotide substitution, or         at least two nucleotide substitutions, or at least three         nucleotide substitutions.     -   20. The expression cassette or expression vector of statement 18         or 19, wherein the promoter is a constitutively active promoter.     -   21. The expression cassette or expression vector of statement         18, 19, or 20, wherein the promoter is an inducible promoter.     -   22. The expression cassette or expression vector of statement         18-20, or 21, wherein the promoter is a prokaryotic promoter.     -   23. A microcompartment comprising the modified polypeptide of         statement 1-16 or 17.     -   24. The microcompartment of statement 23, further comprising one         or more iron atoms.     -   25. The microcompartment of statement 23 or 24, comprising one         or more [4Fe-4S] clusters.     -   26. The microcompartment of statement 23, 24 or 25, comprising a         series of BMC-T trimers.     -   27. The microcompartment of statement 23-25 or 26, comprising a         series of BMC-T1 trimers, each BMC-T having a sequence         comprising at least 95% sequence identity, each with SEQ ID         NO:1, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID         NO:7, or SEQ ID NO:8.     -   28. The microcompartment of statement 23-26 or 27, comprising         one or more BMC-T2 trimer having a sequence comprising at least         95% sequence identity with SEQ ID NO:11.     -   29. The microcompartment of statement 23-27 or 28, comprising         one or more BMC-T3 trimer having a sequence comprising at least         95% sequence identity with SEQ ID NO:13.     -   30. The microcompartment of statement 23-28, or 29, further         comprising a series of BMC-H hexamers.     -   31. The microcompartment of statement 23-29 or 30, comprising a         series of BMC-H hexamers, each BMC-H with a sequence comprising         at least 95% sequence identity with SEQ ID NO:9.     -   32. The microcompartment of statement 23-30 or 31, further         comprising a series of BMC-P pentamers.     -   33. The microcompartment of statement 23-31 or 32, further         comprising further comprising a series of BMC-P pentamers, each         BMC-P having a sequence comprising at least 95% sequence         identity with SEQ ID NO: 15, SEQ ID NO:17, or SEQ ID NO:19.     -   34. The microcompartment of statement 23-32 or 33 comprising: a         modified BMC-T subunit with sequence SEQ ID NO:3-7 or 8, a BMC-T         subunit with sequence SEQ ID NO:11, a BMC-T subunit with         sequence SEQ ID NO:13, a BMC-H subunit with sequence SEQ ID         NO:9, a BMC-P subunit with sequence SEQ ID NO: 15, a BMC-P         subunit with sequence SEQ ID NO: 17, and a BMC-P subunit with         sequence SEQ ID NO: 19.     -   35. The microcompartment of statement 23-33, or 34, which         exhibit a reduction potential of −500 to −200 mV or −455 to −370         mV versus the Standard Hydrogen Electrode (SHE).     -   36. The microcompartment of statement 23-34 or 35, which is         stable through redox cycling.     -   37. The microcompartment of statement 23-35 or 36, further         comprising an encapsulated enzyme.     -   38. The microcompartment of statement 23-36 or 37, further         comprising an encapsulated nitrogenase.     -   39. The microcompartment of statement 23-37 or 38, further         comprising an enzyme of a methylerythritol 4-phosphate (MEP)         pathway.     -   40. The microcompartment of statement 23-37 or 39, further         comprising an IspG and/or IspH enzyme,     -   41. The microcompartment of statement 23-39 or 40, further         comprising an enzyme that can catalyze the conversion of         NAD/NADP.     -   42. A method comprising transforming a host cell with an         expression cassette or expression vector comprising a promoter         operably linked to a nucleotide segment that encodes the         modified polypeptide of statement 1-16 or 17, and culturing the         host cell in a culture medium.     -   43. The method of statement 42, comprising growing the host cell         to generate a population of host cells.     -   44. The method of statement 42 or 43, comprising growing the         host cell to generate a population of host cells and culturing         the population of host cells in a bioreactor.     -   45. A method comprising culturing a host cell comprising the         microcompartment of statement 23-40 or 41.     -   46. The method of statement 45, comprising growing the host cell         to generate a population of host cells.     -   47. The method of statement 45 or 46, comprising growing the         host cell to generate a population of host cells and culturing         the population of host cells in a bioreactor.     -   48. A method comprising incubating the modified polypeptide of         statement 1-16 or 17 with an iron III (Fe⁺³) salt.     -   49. The method of statement 48 further comprising incubating the         modified polypeptide with sulfur (e.g Na₂S) to generate a         modified polypeptide with Fe—S clusters.     -   50. The method of statement 49, further comprising separating         the modified polypeptide with Fe—S clusters from impurities such         as salts, excess iron III (Fe⁺³), excess sulfur, or a         combination thereof.     -   51. A method comprising (a) culturing in a culture medium a         population of host cells comprising an expression cassette or         expression vector comprising a promoter operably linked to a         nucleotide segment that encodes the modified polypeptide of         statement 1-16 or 17, wherein the host cell also comprises an         endogenous gene or a heterologous expression cassette that         encodes an enzyme or a product; and (b) isolating         microcompartments from the population.     -   52. The method of statement 51, wherein the enzyme catalyzes an         oxidation reaction.     -   53. The method of statement 51 or 52, wherein the enzyme is an         aldehyde dehydrogenase, alcohol dehydrogenase, or         phospotransacylase.     -   54. The method of statement 51, 53, or 53, wherein the enzyme         catalyzes one or more reduction/oxidation (redox) reaction.     -   55. The method of statement 51, 53, or 53, wherein the enzyme         catalyzes one or more electron transfer reaction.     -   56. The method of statement 51-54 or 55, further comprising         isolating the product from the microcompartments.     -   57. The method of statement 51-55 or 56, wherein the product is         a small molecule.     -   58. The method of statement 51-56 or 57, wherein the product is         a biofuel.     -   59. The method of statement 51-57 or 58, wherein the product is         an alcohol, amine, alkanolamine, or a combination thereof.     -   60. The method of statement 51-58 or 59, wherein the product is         a propanediol, ethanolamine, amino-2-propanol, or a combination         thereof.

The specific compositions and methods described herein are representative, exemplary and not intended as limitations on the scope of the invention. Other objects, aspects, and embodiments will occur to those skilled in the art upon consideration of this specification, and are encompassed within the spirit of the invention as defined by the scope of the claims. It will be readily apparent to one skilled in the art that varying substitutions and modifications may be made to the invention disclosed herein without departing from the scope and spirit of the invention. The terms and expressions that have been employed are used as terms of description and not of limitation, and there is no intent in the use of such terms and expressions to exclude any equivalent of the features shown and described or portions thereof, but it is recognized that various modifications are possible within the scope of the invention as claimed. Thus, it will be understood that although the present invention has been specifically disclosed by embodiments and optional features, modification and variation of the concepts herein disclosed may be resorted to by those skilled in the art, and that such modifications and variations are considered to be within the scope of this invention as defined by the appended claims and statements of the invention.

The invention illustratively described herein may be practiced in the absence of any element or elements, or limitation or limitations, which is not specifically disclosed herein as essential. The methods and processes illustratively described herein may be practiced in differing orders of steps, and the methods and processes are not necessarily restricted to the orders of steps indicated herein or in the claims.

As used herein and in the appended claims, the singular forms “a.” “an,” and “the” include plural reference unless the context clearly dictates otherwise. Thus, for example, a reference to “a plant” or “a seed” or “a cell” includes a plurality of such plants, seeds or cells, and so forth. In this document, the term “or” is used to refer to a nonexclusive or, such that “A or B” includes “A but not B,” “B but not A,” and “A and B,” unless otherwise indicated.

Under no circumstances may the patent be interpreted to be limited to the specific examples or embodiments or methods specifically disclosed herein. Under no circumstances may the patent be interpreted to be limited by any statement made by any Examiner or any other official or employee of the Patent and Trademark Office unless such statement is specifically and without qualification or reservation expressly adopted in a responsive writing by Applicants.

The invention has been described broadly and generically herein. Each of the narrower species and subgeneric groupings falling within the generic disclosure also form part of the invention. This includes the generic description of the invention with a proviso or negative limitation removing any subject matter from the genus, regardless of whether or not the excised material is specifically recited herein. In addition, where features or aspects of the invention are described in terms of Markush groups, those skilled in the art will recognize that the invention is also thereby described in terms of any individual member or subgroup of members of the Markush group.

The Abstract is provided to comply with 37 C.F.R. § 1.72(b) to allow the reader to quickly ascertain the nature and gist of the technical disclosure. The Abstract is submitted with the understanding that it will not be used to interpret or limit the scope or meaning of the claims. 

What is claimed:
 1. A polypeptide comprising at least 95% sequence identity to SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, or SEQ ID NO:8, and comprising a cysteine substitution at position 55, 56 or at both positions 55 and
 56. 2. A host cell comprising the polypeptide of claim
 1. 3. A bacterial microcompartment comprising the polypeptide of claim
 1. 4. The bacterial microcompartment of claim 3, further comprising at least one BMC-H subunit.
 5. The bacterial microcompartment of claim 4, further comprising an enzyme.
 6. The bacterial microcompartment of claim 5, wherein the enzyme catalyzes an oxidation reaction.
 7. The bacterial microcompartment of claim 3, further comprising at least one BMC-P subunit.
 8. The bacterial microcompartment of claim 3, further comprising one or more BMC-T2 proteins.
 9. The bacterial microcompartment of claim 3, further comprising one or more BMC-T3 proteins.
 10. The bacterial microcompartment of claim 3, further comprising one or more iron atoms.
 11. The bacterial microcompartment of claim 3, further comprising one or more [4Fe-4S] clusters.
 12. The bacterial microcompartment of claim 3, further comprising an enzyme that can catalyze the conversion of NAD/NADP.
 13. A host cell comprising the bacterial microcompartment of claim
 3. 14. The polypeptide of claim 1 wherein the polypeptide comprises a substitution of an amino acid at position 56 or position
 154. 15. The polypeptide of claim 1 wherein the polypeptide comprises a substitution of an amino acid at position 56 and position
 154. 16. The polypeptide of claim 1 wherein the polypeptide comprises a substitution of a serine at position 56 with a cysteine (S56C).
 17. The polypeptide of claim 1 wherein the polypeptide comprises a substitution of an isoleucine at position 154 with a phenylalanine (I154F). 